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MIGSA.Rcheck/tests_i386/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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> BiocGenerics:::testPackage("MIGSA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
INFO [2019-10-16 05:17:58] Downloaded BioCarta_2015
INFO [2019-10-16 05:17:58] Converting Symbol to Entrez
ERROR [2019-10-16 05:18:00] Gene sets file path error, check if it is readable.
ERROR [2019-10-16 05:18:00] Gene sets file path error, check if it is readable.
ERROR [2019-10-16 05:18:00] Gene sets file path error, check if it is readable.
INFO [2019-10-16 05:18:04] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:04] DE genes 5 of a total of 100 ( 5 %)
ERROR [2019-10-16 05:18:04] GeneSetCollection names must be unique
INFO [2019-10-16 05:18:04] *************************************
INFO [2019-10-16 05:18:04] Starting MIGSA analysis.
INFO [2019-10-16 05:18:04] *************************************
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : Starting IGSA analysis.
INFO [2019-10-16 05:18:04] 10 Gene Sets.
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : dEnricher starting.
INFO [2019-10-16 05:18:04] DE genes 10
INFO [2019-10-16 05:18:04] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:04] Running SEA at cores: 1
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : dEnricher finnished.
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : mGSZ starting.
INFO [2019-10-16 05:18:04] Number of unique permutations: 2
INFO [2019-10-16 05:18:04] Getting ranking at cores: 1
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : mGSZ finnished.
INFO [2019-10-16 05:18:04] MIGSA_ok_manuallyDEGenes : IGSA analysis ended.
INFO [2019-10-16 05:18:05] *************************************
INFO [2019-10-16 05:18:05] Starting MIGSA analysis.
INFO [2019-10-16 05:18:05] *************************************
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : Starting IGSA analysis.
INFO [2019-10-16 05:18:05] 10 Gene Sets.
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : dEnricher starting.
INFO [2019-10-16 05:18:05] DE genes 0 of a total of 200 ( 0 %)
INFO [2019-10-16 05:18:05] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:05] Running SEA at cores: 1
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : dEnricher finnished.
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : mGSZ starting.
INFO [2019-10-16 05:18:05] Number of unique permutations: 3
INFO [2019-10-16 05:18:05] Getting ranking at cores: 1
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : mGSZ finnished.
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWNoDE : IGSA analysis ended.
INFO [2019-10-16 05:18:05] *************************************
INFO [2019-10-16 05:18:05] Starting MIGSA analysis.
INFO [2019-10-16 05:18:05] *************************************
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWtwoPerm : Starting IGSA analysis.
INFO [2019-10-16 05:18:05] 10 Gene Sets.
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWtwoPerm : dEnricher starting.
INFO [2019-10-16 05:18:05] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:05] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:05] Running SEA at cores: 1
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWtwoPerm : dEnricher finnished.
INFO [2019-10-16 05:18:05] MIGSA_ok_noErrorWtwoPerm : mGSZ starting.
INFO [2019-10-16 05:18:05] Number of unique permutations: 2
INFO [2019-10-16 05:18:05] Getting ranking at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_noErrorWtwoPerm : mGSZ finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_noErrorWtwoPerm : IGSA analysis ended.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] Starting MIGSA analysis.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : Starting IGSA analysis.
INFO [2019-10-16 05:18:06] 10 Gene Sets.
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : dEnricher starting.
INFO [2019-10-16 05:18:06] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:06] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:06] Running SEA at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : dEnricher finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : mGSZ starting.
INFO [2019-10-16 05:18:06] Number of unique permutations: 3
INFO [2019-10-16 05:18:06] Getting ranking at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : mGSZ finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_oneExp : IGSA analysis ended.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] Starting MIGSA analysis.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:06] 10 Gene Sets.
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : dEnricher starting.
INFO [2019-10-16 05:18:06] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:06] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:06] Running SEA at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : dEnricher finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : mGSZ starting.
INFO [2019-10-16 05:18:06] Number of unique permutations: 5
INFO [2019-10-16 05:18:06] Getting ranking at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : mGSZ finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea1 : IGSA analysis ended.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] Starting MIGSA analysis.
INFO [2019-10-16 05:18:06] *************************************
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:06] 10 Gene Sets.
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea2 : dEnricher starting.
INFO [2019-10-16 05:18:06] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:06] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:06] Running SEA at cores: 1
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea2 : dEnricher finnished.
INFO [2019-10-16 05:18:06] MIGSA_ok_onlySeaOrGsea2 : IGSA analysis ended.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] Starting MIGSA analysis.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] MIGSA_ok_paramsCantbebothNull : Starting IGSA analysis.
INFO [2019-10-16 05:18:07] 10 Gene Sets.
Error in IGSA(igsaInput) : SEAparams and GSEAparams are both NULL
In addition: Warning messages:
1: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
2: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
3: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
WARN [2019-10-16 05:18:07] 1 experiments had errors
WARN [2019-10-16 05:18:07] MIGSA_ok_paramsCantbebothNull had errors
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] Starting MIGSA analysis.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:07] 4 Gene Sets.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : dEnricher starting.
INFO [2019-10-16 05:18:07] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:07] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:07] Running SEA at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : dEnricher finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : mGSZ starting.
INFO [2019-10-16 05:18:07] Number of unique permutations: 4
INFO [2019-10-16 05:18:07] Getting ranking at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : mGSZ finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp1 : IGSA analysis ended.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:07] 4 Gene Sets.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : dEnricher starting.
INFO [2019-10-16 05:18:07] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:07] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:07] Running SEA at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : dEnricher finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : mGSZ starting.
INFO [2019-10-16 05:18:07] Number of unique permutations: 5
INFO [2019-10-16 05:18:07] Getting ranking at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : mGSZ finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExp2 : IGSA analysis ended.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] Starting MIGSA analysis.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:07] 8 Gene Sets.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : dEnricher starting.
INFO [2019-10-16 05:18:07] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:07] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:07] Running SEA at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : dEnricher finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : mGSZ starting.
INFO [2019-10-16 05:18:07] Number of unique permutations: 4
INFO [2019-10-16 05:18:07] Getting ranking at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : mGSZ finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs1 : IGSA analysis ended.
INFO [2019-10-16 05:18:07] *************************************
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:07] 8 Gene Sets.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : dEnricher starting.
INFO [2019-10-16 05:18:07] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:07] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:07] Running SEA at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : dEnricher finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : mGSZ starting.
INFO [2019-10-16 05:18:07] Number of unique permutations: 5
INFO [2019-10-16 05:18:07] Getting ranking at cores: 1
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : mGSZ finnished.
INFO [2019-10-16 05:18:07] MIGSA_ok_twoExpFourGSs2 : IGSA analysis ended.
INFO [2019-10-16 05:18:08] *************************************
INFO [2019-10-16 05:18:08] Starting MIGSA analysis.
INFO [2019-10-16 05:18:08] *************************************
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:08] 8 Gene Sets.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : dEnricher starting.
INFO [2019-10-16 05:18:08] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:08] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:08] Running SEA at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : dEnricher finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : mGSZ starting.
INFO [2019-10-16 05:18:08] Number of unique permutations: 4
INFO [2019-10-16 05:18:08] Getting ranking at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : mGSZ finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs1 : IGSA analysis ended.
INFO [2019-10-16 05:18:08] *************************************
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:08] 8 Gene Sets.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : dEnricher starting.
INFO [2019-10-16 05:18:08] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:08] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:08] Running SEA at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : dEnricher finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : mGSZ starting.
INFO [2019-10-16 05:18:08] Number of unique permutations: 5
INFO [2019-10-16 05:18:08] Getting ranking at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : mGSZ finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoExptwoGSs2 : IGSA analysis ended.
INFO [2019-10-16 05:18:08] *************************************
INFO [2019-10-16 05:18:08] Starting MIGSA analysis.
INFO [2019-10-16 05:18:08] *************************************
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : Starting IGSA analysis.
INFO [2019-10-16 05:18:08] 20 Gene Sets.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : dEnricher starting.
INFO [2019-10-16 05:18:08] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:08] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:08] Running SEA at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : dEnricher finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : mGSZ starting.
INFO [2019-10-16 05:18:08] Number of unique permutations: 5
INFO [2019-10-16 05:18:08] Getting ranking at cores: 1
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : mGSZ finnished.
INFO [2019-10-16 05:18:08] MIGSA_ok_twoGSs : IGSA analysis ended.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] Starting MIGSA analysis.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:09] 10 Gene Sets.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : dEnricher starting.
INFO [2019-10-16 05:18:09] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:09] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:09] Running SEA at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : dEnricher finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : mGSZ starting.
INFO [2019-10-16 05:18:09] Number of unique permutations: 2
INFO [2019-10-16 05:18:09] Getting ranking at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : mGSZ finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests1 : IGSA analysis ended.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] Starting MIGSA analysis.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:09] 10 Gene Sets.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : dEnricher starting.
INFO [2019-10-16 05:18:09] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:09] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:09] Running SEA at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : dEnricher finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : mGSZ starting.
INFO [2019-10-16 05:18:09] Number of unique permutations: 2
INFO [2019-10-16 05:18:09] Getting ranking at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : mGSZ finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests2 : IGSA analysis ended.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] Starting MIGSA analysis.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : Starting IGSA analysis.
INFO [2019-10-16 05:18:09] 10 Gene Sets.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : dEnricher starting.
INFO [2019-10-16 05:18:09] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:09] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:09] Running SEA at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : dEnricher finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : mGSZ starting.
INFO [2019-10-16 05:18:09] Number of unique permutations: 2
INFO [2019-10-16 05:18:09] Getting ranking at cores: 1
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : mGSZ finnished.
INFO [2019-10-16 05:18:09] MIGSA_ok_useDifferenttests3 : IGSA analysis ended.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] Starting MIGSA analysis.
INFO [2019-10-16 05:18:09] *************************************
INFO [2019-10-16 05:18:09] MIGSA_ok_useOwnbr1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:09] 10 Gene Sets.
INFO [2019-10-16 05:18:09] MIGSA_ok_useOwnbr1 : dEnricher starting.
INFO [2019-10-16 05:18:09] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:09] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:10] Running SEA at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr1 : dEnricher finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr1 : mGSZ starting.
INFO [2019-10-16 05:18:10] Number of unique permutations: 2
INFO [2019-10-16 05:18:10] Getting ranking at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr1 : mGSZ finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr1 : IGSA analysis ended.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] Starting MIGSA analysis.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:10] 10 Gene Sets.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : dEnricher starting.
INFO [2019-10-16 05:18:10] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:10] Using user provided BR: 1000 genes.
INFO [2019-10-16 05:18:10] Running SEA at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : dEnricher finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : mGSZ starting.
INFO [2019-10-16 05:18:10] Number of unique permutations: 2
INFO [2019-10-16 05:18:10] Getting ranking at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : mGSZ finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbr2 : IGSA analysis ended.
INFO [2019-10-16 05:18:10] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] Starting MIGSA analysis.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:10] 10 Gene Sets.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData1 : dEnricher starting.
INFO [2019-10-16 05:18:10] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:10] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:10] Running SEA at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData1 : dEnricher finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData1 : IGSA analysis ended.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] Starting MIGSA analysis.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:10] 10 Gene Sets.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData2 : dEnricher starting.
INFO [2019-10-16 05:18:10] DE genes 9
INFO [2019-10-16 05:18:10] Using user provided BR: 200 genes.
INFO [2019-10-16 05:18:10] Running SEA at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData2 : dEnricher finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_useOwnbrNoExprData2 : IGSA analysis ended.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] Starting MIGSA analysis.
INFO [2019-10-16 05:18:10] *************************************
INFO [2019-10-16 05:18:10] MIGSA_ok_usebri1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:10] 10 Gene Sets.
INFO [2019-10-16 05:18:10] MIGSA_ok_usebri1 : dEnricher starting.
INFO [2019-10-16 05:18:10] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:10] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:10] Running SEA at cores: 1
INFO [2019-10-16 05:18:10] MIGSA_ok_usebri1 : dEnricher finnished.
INFO [2019-10-16 05:18:10] MIGSA_ok_usebri1 : mGSZ starting.
INFO [2019-10-16 05:18:10] Number of unique permutations: 2
INFO [2019-10-16 05:18:10] Getting ranking at cores: 1
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri1 : mGSZ finnished.
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri1 : IGSA analysis ended.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:11] 10 Gene Sets.
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : dEnricher starting.
INFO [2019-10-16 05:18:11] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:11] Using BRI: 100 genes.
INFO [2019-10-16 05:18:11] Running SEA at cores: 1
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : dEnricher finnished.
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : mGSZ starting.
INFO [2019-10-16 05:18:11] Number of unique permutations: 2
INFO [2019-10-16 05:18:11] Getting ranking at cores: 1
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : mGSZ finnished.
INFO [2019-10-16 05:18:11] MIGSA_ok_usebri2 : IGSA analysis ended.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] MIGSA_ok_wrongbrOption : Starting IGSA analysis.
INFO [2019-10-16 05:18:11] 10 Gene Sets.
INFO [2019-10-16 05:18:11] MIGSA_ok_wrongbrOption : dEnricher starting.
INFO [2019-10-16 05:18:11] DE genes 9 of a total of 200 ( 4.5 %)
Error in DEnricher(seaParams(igsaInput), expr_data, fit_options, merged_gene_sets) :
Incorrect br option.
In addition: Warning messages:
1: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
2: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
3: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
WARN [2019-10-16 05:18:11] 1 experiments had errors
WARN [2019-10-16 05:18:11] MIGSA_ok_wrongbrOption had errors
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] MIGSA_wrong_noGSets : Starting IGSA analysis.
Error in IGSA(igsaInput) : No gene sets provided.
WARN [2019-10-16 05:18:11] 1 experiments had errors
WARN [2019-10-16 05:18:11] MIGSA_wrong_noGSets had errors
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] *************************************
INFO [2019-10-16 05:18:11] Starting MIGSA analysis.
INFO [2019-10-16 05:18:11] Number of unique permutations: 6
INFO [2019-10-16 05:18:11] Getting ranking at cores: 1
INFO [2019-10-16 05:18:12] Gene sets enriched in 0 experiments: 186
INFO [2019-10-16 05:18:12] Gene sets enriched in 1 experiments: 14
id Name GS_Name igsaInput1 igsaInput2
1 set1 myGeneSets 0.9914680853 0.4168966300
2 set10 myGeneSets 0.2077634588 0.7604938133
3 set100 myGeneSets 0.6524399615 0.2636081104
4 set101 myGeneSets 0.6028661233 0.7819407689
5 set102 myGeneSets 0.2075885961 0.8634517316
6 set103 myGeneSets 0.9675421042 0.6434408170
7 set104 myGeneSets 0.9849658621 0.8785750164
8 set105 myGeneSets 0.7278610208 0.6978651389
9 set106 myGeneSets 0.0976892057 0.0968769667
10 set107 myGeneSets 0.2721506900 0.2636081104
11 set108 myGeneSets 0.3991092243 0.9495912592
12 set109 myGeneSets 0.0012578955 0.1343382494
13 set11 myGeneSets 0.2325245221 0.1220288916
14 set110 myGeneSets 0.6646992155 0.0048841759
15 set111 myGeneSets 0.2766796796 0.0285823191
16 set112 myGeneSets 0.6660154454 0.2636081104
17 set113 myGeneSets 0.4400743046 0.7241909782
18 set114 myGeneSets 0.9397402270 0.7346948547
19 set115 myGeneSets 0.2325245221 0.2002922056
20 set116 myGeneSets 0.0004180150 0.8727164292
21 set117 myGeneSets 0.4744175398 0.6423134692
22 set118 myGeneSets 0.6519093256 0.2636081104
23 set119 myGeneSets 0.6185708274 0.1293207416
24 set12 myGeneSets 0.8550929366 0.8536352844
25 set120 myGeneSets 0.3793668855 0.3919750079
26 set121 myGeneSets 0.8931401447 0.1034908565
27 set122 myGeneSets 0.9116149136 0.1903054796
28 set123 myGeneSets 0.0508873429 0.0103128205
29 set124 myGeneSets 0.1833337390 0.2283248086
30 set125 myGeneSets 0.7799284054 0.7481653705
31 set126 myGeneSets 0.4429773329 0.8944594825
32 set127 myGeneSets 0.2378326042 0.2973873962
33 set128 myGeneSets 0.8263980501 0.2344423956
34 set129 myGeneSets 0.0191149083 0.3980301604
35 set13 myGeneSets 0.0671403617 0.1812969067
36 set130 myGeneSets 0.9164398103 0.0337251063
37 set131 myGeneSets 0.7505594526 0.2636081104
38 set132 myGeneSets 0.4410521136 0.0617017284
39 set133 myGeneSets 0.3088933371 0.2433263286
40 set134 myGeneSets 0.0747698640 0.3825203010
41 set135 myGeneSets 0.8926505529 0.6776995008
42 set136 myGeneSets 0.1133099383 0.1093459212
43 set137 myGeneSets 0.0257435644 0.1156289328
44 set138 myGeneSets 0.3506069480 0.4360583151
45 set139 myGeneSets 0.1533377996 0.2118871268
46 set14 myGeneSets 0.1188460709 0.5998744759
47 set140 myGeneSets 0.9327233023 0.7782038257
48 set141 myGeneSets 0.9034092737 0.0025403537
49 set142 myGeneSets 0.3139527474 0.0765378155
50 set143 myGeneSets 0.8845664673 0.2636081104
51 set144 myGeneSets 0.3395232735 0.0848710227
52 set145 myGeneSets 0.6478460166 0.1627288229
53 set146 myGeneSets 0.6769878191 0.0070242334
54 set147 myGeneSets 0.8995076570 0.7562516206
55 set148 myGeneSets 0.1373644318 0.8478977499
56 set149 myGeneSets 0.2587133577 0.0008152734
57 set15 myGeneSets 0.6199859807 0.1505221563
58 set150 myGeneSets 0.9969071636 0.3127243231
59 set151 myGeneSets 0.0306639402 0.1385596555
60 set152 myGeneSets 0.1080089918 0.6612838585
61 set153 myGeneSets 0.2325245221 0.8383027804
62 set154 myGeneSets 0.0844954775 0.1133601701
63 set155 myGeneSets 0.7311495820 0.9710670707
64 set156 myGeneSets 0.2325245221 0.6439016956
65 set157 myGeneSets 0.7028765964 0.7849739488
66 set158 myGeneSets 0.9036459359 0.6381604709
67 set159 myGeneSets 0.0182549109 0.3162486650
68 set16 myGeneSets 0.9441334365 0.0625846850
69 set160 myGeneSets 0.4686467331 0.9147440611
70 set161 myGeneSets 0.1331100595 0.0828723811
71 set162 myGeneSets 0.2489373481 0.0324472931
72 set163 myGeneSets 0.0532882047 0.5650531784
73 set164 myGeneSets 0.6976060057 0.5437606734
74 set165 myGeneSets 0.1701308457 0.3786395275
75 set166 myGeneSets 0.7049160548 0.1935983950
76 set167 myGeneSets 0.5354376389 0.6149344293
77 set168 myGeneSets 0.1553155521 0.7877357584
78 set169 myGeneSets 0.9682384817 0.2821725706
79 set17 myGeneSets 0.2357392613 0.5915612490
80 set170 myGeneSets 0.1800025505 0.7196690468
81 set171 myGeneSets 0.0652899683 0.1234583372
82 set172 myGeneSets 0.1541809580 0.3060607994
83 set173 myGeneSets 0.1938456751 0.5649862770
84 set174 myGeneSets 0.1686407456 0.0315782160
85 set175 myGeneSets 0.0846562856 0.1188518691
86 set176 myGeneSets 0.0026571347 0.9761734821
87 set177 myGeneSets 0.6223420232 0.9426735363
88 set178 myGeneSets 0.8792629190 0.1543905536
89 set179 myGeneSets 0.6747578830 0.1144618508
90 set18 myGeneSets 0.6972242878 0.8949072050
91 set180 myGeneSets 0.6609210072 0.8856232213
92 set181 myGeneSets 0.4844967802 0.8729520480
93 set182 myGeneSets 0.1828937162 0.9945898436
94 set183 myGeneSets 0.2325245221 0.3915162900
95 set184 myGeneSets 0.2350732418 0.0945041618
96 set185 myGeneSets 0.0306561987 0.7161333091
97 set186 myGeneSets 0.8299379225 0.0211508927
98 set187 myGeneSets 0.3633989897 0.2636081104
99 set188 myGeneSets 0.2325245221 0.0025403537
100 set189 myGeneSets 0.4351394588 0.0259416309
101 set19 myGeneSets 0.0806036145 0.0807907043
102 set190 myGeneSets 0.2325245221 0.0767486650
103 set191 myGeneSets 0.7413785584 0.6159433083
104 set192 myGeneSets 0.4037529765 0.1648618781
105 set193 myGeneSets 0.7275129252 0.0597811570
106 set194 myGeneSets 0.8599101661 0.0382544043
107 set195 myGeneSets 0.8726950894 0.8217773455
108 set196 myGeneSets 0.5779079861 0.6236190306
109 set197 myGeneSets 0.0072944335 0.2636081104
110 set198 myGeneSets 0.1673099916 0.0337251063
111 set199 myGeneSets 0.2325245221 0.2636081104
112 set2 myGeneSets 0.9467453016 0.0204620793
113 set20 myGeneSets 0.3674051026 0.8993025670
114 set200 myGeneSets 0.0004774665 0.9172041181
115 set21 myGeneSets 0.8201901985 0.4729573991
116 set22 myGeneSets 0.1115516769 0.2636081104
117 set23 myGeneSets 0.9149239934 0.6801083548
118 set24 myGeneSets 0.8552306435 0.3999973051
119 set25 myGeneSets 0.6726173944 0.1726171015
120 set26 myGeneSets 0.3389275559 0.2019972225
121 set27 myGeneSets 0.9743070454 0.1341676161
122 set28 myGeneSets 0.6029492827 0.1893462049
123 set29 myGeneSets 0.2100309165 0.4175269585
124 set3 myGeneSets 0.3879637562 0.0072158580
125 set30 myGeneSets 0.2325245221 0.0509307325
126 set31 myGeneSets 0.3875964808 0.0480790484
127 set32 myGeneSets 0.2468863267 0.5482852513
128 set33 myGeneSets 0.0263061255 0.0038030260
129 set34 myGeneSets 0.0755101086 0.6999320946
130 set35 myGeneSets 0.3663517537 0.1668681380
131 set36 myGeneSets 0.2325245221 0.0337251063
132 set37 myGeneSets 0.0016619311 0.2636081104
133 set38 myGeneSets 0.8489631930 0.4084607480
134 set39 myGeneSets 0.5522477107 0.7391784048
135 set4 myGeneSets 0.9335442444 0.2636081104
136 set40 myGeneSets 0.2325245221 0.2636081104
137 set41 myGeneSets 0.4763762069 0.2254261790
138 set42 myGeneSets 0.0126301418 0.6930395372
139 set43 myGeneSets 0.3798400922 0.1266492135
140 set44 myGeneSets 0.2325245221 0.1394188193
141 set45 myGeneSets 0.6620019985 0.0890050925
142 set46 myGeneSets 0.2325245221 0.9426411416
143 set47 myGeneSets 0.1124578652 0.9816946638
144 set48 myGeneSets 0.8425070349 0.2053180739
145 set49 myGeneSets 0.8632151812 0.7314909064
146 set5 myGeneSets 0.0818141664 0.3818603552
147 set50 myGeneSets 0.9215449879 0.8590358443
148 set51 myGeneSets 0.6362625813 0.6121783056
149 set52 myGeneSets 0.5467404688 0.8410637728
150 set53 myGeneSets 0.4499763142 0.8026402330
151 set54 myGeneSets 0.2325245221 0.7176210502
152 set55 myGeneSets 0.0778172813 0.1488708302
153 set56 myGeneSets 0.6932611585 0.0098365760
154 set57 myGeneSets 0.3412720183 0.7787995350
155 set58 myGeneSets 0.9148574195 0.2636081104
156 set59 myGeneSets 0.1554817168 0.2075876600
157 set6 myGeneSets 0.8288302160 0.4269604520
158 set60 myGeneSets 0.7004109327 0.7009680745
159 set61 myGeneSets 0.0257435644 0.2636081104
160 set62 myGeneSets 0.5594080390 0.2636081104
161 set63 myGeneSets 0.3544279599 0.2636081104
162 set64 myGeneSets 0.4659211160 0.6806334019
163 set65 myGeneSets 0.7703370283 0.2678343420
164 set66 myGeneSets 0.8455749956 0.6833387245
165 set67 myGeneSets 0.6351691930 0.9293771610
166 set68 myGeneSets 0.8873273715 0.1642212629
167 set69 myGeneSets 0.6586275711 0.2405258305
168 set7 myGeneSets 0.2625428482 0.2636081104
169 set70 myGeneSets 0.2325245221 0.5931253640
170 set71 myGeneSets 0.0878540376 0.0232157689
171 set72 myGeneSets 0.1741649934 0.1849660763
172 set73 myGeneSets 0.7633023538 0.9416729567
173 set74 myGeneSets 0.0867563437 0.2636081104
174 set75 myGeneSets 0.8709992962 0.0858845718
175 set76 myGeneSets 0.2325245221 0.4750379273
176 set77 myGeneSets 0.0984344452 0.3778709683
177 set78 myGeneSets 0.8630192935 0.0424942618
178 set79 myGeneSets 0.8933633628 0.2604480883
179 set8 myGeneSets 0.2325245221 0.3543968025
180 set80 myGeneSets 0.9775811773 0.0337251063
181 set81 myGeneSets 0.0179728884 0.3842944699
182 set82 myGeneSets 0.1373931570 0.6549650313
183 set83 myGeneSets 0.2325245221 0.1491929017
184 set84 myGeneSets 0.2810828326 0.2099679276
185 set85 myGeneSets 0.2928053872 0.2636081104
186 set86 myGeneSets 0.9670592552 0.1298954445
187 set87 myGeneSets 0.3556141919 0.9408833834
188 set88 myGeneSets 0.7661234566 0.2531155642
189 set89 myGeneSets 0.8533546654 0.3701744384
190 set9 myGeneSets 0.2631788445 0.4256747832
191 set90 myGeneSets 0.7219530942 0.9620316887
192 set91 myGeneSets 0.0883950480 0.5610455932
193 set92 myGeneSets 0.7898776660 0.1922651204
194 set93 myGeneSets 0.1376995687 0.1111976766
195 set94 myGeneSets 0.6926679462 0.9141710458
196 set95 myGeneSets 0.2325245221 0.0529390033
197 set96 myGeneSets 0.1525256696 0.4954544930
198 set97 myGeneSets 0.8118502439 0.7513042427
199 set98 myGeneSets 0.5386436490 0.8443455662
200 set99 myGeneSets 0.5017492400 0.1614411097
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
RUNIT TEST PROTOCOL -- Wed Oct 16 05:18:21 2019
***********************************************
Number of test functions: 87
Number of errors: 0
Number of failures: 0
1 Test Suite :
MIGSA RUnit Tests - 87 test functions, 0 errors, 0 failures
Number of test functions: 87
Number of errors: 0
Number of failures: 0
Warning messages:
1: In filterByGenes(migsaRes, "") :
Provided genes did not contribute to enrich any gene set.
2: In filterByGenes(migsaRes, c("fakeGene1", "fakeGene2")) :
Provided genes did not contribute to enrich any gene set.
3: In filterByGenes(migsaRes, impGenes) :
No enriched gene set with used cutOff.
4: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
5: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
6: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
>
> proc.time()
user system elapsed
29.42 2.84 35.17
|
MIGSA.Rcheck/tests_x64/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("MIGSA")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: BiocParallel
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
INFO [2019-10-16 05:18:32] Downloaded BioCarta_2015
INFO [2019-10-16 05:18:32] Converting Symbol to Entrez
ERROR [2019-10-16 05:18:34] Gene sets file path error, check if it is readable.
ERROR [2019-10-16 05:18:34] Gene sets file path error, check if it is readable.
ERROR [2019-10-16 05:18:34] Gene sets file path error, check if it is readable.
INFO [2019-10-16 05:18:37] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:37] DE genes 5 of a total of 100 ( 5 %)
ERROR [2019-10-16 05:18:37] GeneSetCollection names must be unique
INFO [2019-10-16 05:18:37] *************************************
INFO [2019-10-16 05:18:37] Starting MIGSA analysis.
INFO [2019-10-16 05:18:37] *************************************
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : Starting IGSA analysis.
INFO [2019-10-16 05:18:37] 10 Gene Sets.
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : dEnricher starting.
INFO [2019-10-16 05:18:37] DE genes 10
INFO [2019-10-16 05:18:37] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:37] Running SEA at cores: 1
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : dEnricher finnished.
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : mGSZ starting.
INFO [2019-10-16 05:18:37] Number of unique permutations: 2
INFO [2019-10-16 05:18:37] Getting ranking at cores: 1
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : mGSZ finnished.
INFO [2019-10-16 05:18:37] MIGSA_ok_manuallyDEGenes : IGSA analysis ended.
INFO [2019-10-16 05:18:37] *************************************
INFO [2019-10-16 05:18:37] Starting MIGSA analysis.
INFO [2019-10-16 05:18:37] *************************************
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : Starting IGSA analysis.
INFO [2019-10-16 05:18:37] 10 Gene Sets.
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : dEnricher starting.
INFO [2019-10-16 05:18:37] DE genes 0 of a total of 200 ( 0 %)
INFO [2019-10-16 05:18:37] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:37] Running SEA at cores: 1
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : dEnricher finnished.
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : mGSZ starting.
INFO [2019-10-16 05:18:37] Number of unique permutations: 3
INFO [2019-10-16 05:18:37] Getting ranking at cores: 1
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : mGSZ finnished.
INFO [2019-10-16 05:18:37] MIGSA_ok_noErrorWNoDE : IGSA analysis ended.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] Starting MIGSA analysis.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : Starting IGSA analysis.
INFO [2019-10-16 05:18:38] 10 Gene Sets.
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : dEnricher starting.
INFO [2019-10-16 05:18:38] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:38] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:38] Running SEA at cores: 1
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : dEnricher finnished.
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : mGSZ starting.
INFO [2019-10-16 05:18:38] Number of unique permutations: 2
INFO [2019-10-16 05:18:38] Getting ranking at cores: 1
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : mGSZ finnished.
INFO [2019-10-16 05:18:38] MIGSA_ok_noErrorWtwoPerm : IGSA analysis ended.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] Starting MIGSA analysis.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : Starting IGSA analysis.
INFO [2019-10-16 05:18:38] 10 Gene Sets.
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : dEnricher starting.
INFO [2019-10-16 05:18:38] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:38] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:38] Running SEA at cores: 1
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : dEnricher finnished.
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : mGSZ starting.
INFO [2019-10-16 05:18:38] Number of unique permutations: 3
INFO [2019-10-16 05:18:38] Getting ranking at cores: 1
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : mGSZ finnished.
INFO [2019-10-16 05:18:38] MIGSA_ok_oneExp : IGSA analysis ended.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] Starting MIGSA analysis.
INFO [2019-10-16 05:18:38] *************************************
INFO [2019-10-16 05:18:38] MIGSA_ok_onlySeaOrGsea1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:38] 10 Gene Sets.
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea1 : dEnricher starting.
INFO [2019-10-16 05:18:39] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:39] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:39] Running SEA at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea1 : dEnricher finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea1 : mGSZ starting.
INFO [2019-10-16 05:18:39] Number of unique permutations: 5
INFO [2019-10-16 05:18:39] Getting ranking at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea1 : mGSZ finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea1 : IGSA analysis ended.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] Starting MIGSA analysis.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:39] 10 Gene Sets.
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea2 : dEnricher starting.
INFO [2019-10-16 05:18:39] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:39] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:39] Running SEA at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea2 : dEnricher finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_onlySeaOrGsea2 : IGSA analysis ended.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] Starting MIGSA analysis.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] MIGSA_ok_paramsCantbebothNull : Starting IGSA analysis.
INFO [2019-10-16 05:18:39] 10 Gene Sets.
Error in IGSA(igsaInput) : SEAparams and GSEAparams are both NULL
In addition: Warning messages:
1: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
2: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
3: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
WARN [2019-10-16 05:18:39] 1 experiments had errors
WARN [2019-10-16 05:18:39] MIGSA_ok_paramsCantbebothNull had errors
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] Starting MIGSA analysis.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:39] 4 Gene Sets.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : dEnricher starting.
INFO [2019-10-16 05:18:39] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:39] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:39] Running SEA at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : dEnricher finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : mGSZ starting.
INFO [2019-10-16 05:18:39] Number of unique permutations: 4
INFO [2019-10-16 05:18:39] Getting ranking at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : mGSZ finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp1 : IGSA analysis ended.
INFO [2019-10-16 05:18:39] *************************************
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:39] 4 Gene Sets.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : dEnricher starting.
INFO [2019-10-16 05:18:39] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:39] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:39] Running SEA at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : dEnricher finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : mGSZ starting.
INFO [2019-10-16 05:18:39] Number of unique permutations: 5
INFO [2019-10-16 05:18:39] Getting ranking at cores: 1
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : mGSZ finnished.
INFO [2019-10-16 05:18:39] MIGSA_ok_twoExp2 : IGSA analysis ended.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] Starting MIGSA analysis.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:40] 8 Gene Sets.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : dEnricher starting.
INFO [2019-10-16 05:18:40] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:40] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:40] Running SEA at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : dEnricher finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : mGSZ starting.
INFO [2019-10-16 05:18:40] Number of unique permutations: 4
INFO [2019-10-16 05:18:40] Getting ranking at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : mGSZ finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs1 : IGSA analysis ended.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:40] 8 Gene Sets.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : dEnricher starting.
INFO [2019-10-16 05:18:40] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:40] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:40] Running SEA at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : dEnricher finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : mGSZ starting.
INFO [2019-10-16 05:18:40] Number of unique permutations: 5
INFO [2019-10-16 05:18:40] Getting ranking at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : mGSZ finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExpFourGSs2 : IGSA analysis ended.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] Starting MIGSA analysis.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:40] 8 Gene Sets.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : dEnricher starting.
INFO [2019-10-16 05:18:40] DE genes 0 of a total of 100 ( 0 %)
INFO [2019-10-16 05:18:40] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:40] Running SEA at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : dEnricher finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : mGSZ starting.
INFO [2019-10-16 05:18:40] Number of unique permutations: 4
INFO [2019-10-16 05:18:40] Getting ranking at cores: 1
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : mGSZ finnished.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs1 : IGSA analysis ended.
INFO [2019-10-16 05:18:40] *************************************
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:40] 8 Gene Sets.
INFO [2019-10-16 05:18:40] MIGSA_ok_twoExptwoGSs2 : dEnricher starting.
INFO [2019-10-16 05:18:40] DE genes 1 of a total of 100 ( 1 %)
INFO [2019-10-16 05:18:41] Using BRIII: 100 genes.
INFO [2019-10-16 05:18:41] Running SEA at cores: 1
INFO [2019-10-16 05:18:41] MIGSA_ok_twoExptwoGSs2 : dEnricher finnished.
INFO [2019-10-16 05:18:41] MIGSA_ok_twoExptwoGSs2 : mGSZ starting.
INFO [2019-10-16 05:18:41] Number of unique permutations: 5
INFO [2019-10-16 05:18:41] Getting ranking at cores: 1
INFO [2019-10-16 05:18:41] MIGSA_ok_twoExptwoGSs2 : mGSZ finnished.
INFO [2019-10-16 05:18:41] MIGSA_ok_twoExptwoGSs2 : IGSA analysis ended.
INFO [2019-10-16 05:18:41] *************************************
INFO [2019-10-16 05:18:41] Starting MIGSA analysis.
INFO [2019-10-16 05:18:41] *************************************
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : Starting IGSA analysis.
INFO [2019-10-16 05:18:41] 20 Gene Sets.
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : dEnricher starting.
INFO [2019-10-16 05:18:41] DE genes 1 of a total of 200 ( 0.5 %)
INFO [2019-10-16 05:18:41] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:41] Running SEA at cores: 1
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : dEnricher finnished.
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : mGSZ starting.
INFO [2019-10-16 05:18:41] Number of unique permutations: 5
INFO [2019-10-16 05:18:41] Getting ranking at cores: 1
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : mGSZ finnished.
INFO [2019-10-16 05:18:41] MIGSA_ok_twoGSs : IGSA analysis ended.
INFO [2019-10-16 05:18:41] *************************************
INFO [2019-10-16 05:18:41] Starting MIGSA analysis.
INFO [2019-10-16 05:18:41] *************************************
INFO [2019-10-16 05:18:41] MIGSA_ok_useDifferenttests1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:41] 10 Gene Sets.
INFO [2019-10-16 05:18:41] MIGSA_ok_useDifferenttests1 : dEnricher starting.
INFO [2019-10-16 05:18:41] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:41] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:41] Running SEA at cores: 1
INFO [2019-10-16 05:18:41] MIGSA_ok_useDifferenttests1 : dEnricher finnished.
INFO [2019-10-16 05:18:41] MIGSA_ok_useDifferenttests1 : mGSZ starting.
INFO [2019-10-16 05:18:41] Number of unique permutations: 2
INFO [2019-10-16 05:18:41] Getting ranking at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests1 : mGSZ finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests1 : IGSA analysis ended.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] Starting MIGSA analysis.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:42] 10 Gene Sets.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : dEnricher starting.
INFO [2019-10-16 05:18:42] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:42] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:42] Running SEA at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : dEnricher finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : mGSZ starting.
INFO [2019-10-16 05:18:42] Number of unique permutations: 2
INFO [2019-10-16 05:18:42] Getting ranking at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : mGSZ finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests2 : IGSA analysis ended.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] Starting MIGSA analysis.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : Starting IGSA analysis.
INFO [2019-10-16 05:18:42] 10 Gene Sets.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : dEnricher starting.
INFO [2019-10-16 05:18:42] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:42] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:42] Running SEA at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : dEnricher finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : mGSZ starting.
INFO [2019-10-16 05:18:42] Number of unique permutations: 2
INFO [2019-10-16 05:18:42] Getting ranking at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : mGSZ finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useDifferenttests3 : IGSA analysis ended.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] Starting MIGSA analysis.
INFO [2019-10-16 05:18:42] *************************************
INFO [2019-10-16 05:18:42] MIGSA_ok_useOwnbr1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:42] 10 Gene Sets.
INFO [2019-10-16 05:18:42] MIGSA_ok_useOwnbr1 : dEnricher starting.
INFO [2019-10-16 05:18:42] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:42] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:42] Running SEA at cores: 1
INFO [2019-10-16 05:18:42] MIGSA_ok_useOwnbr1 : dEnricher finnished.
INFO [2019-10-16 05:18:42] MIGSA_ok_useOwnbr1 : mGSZ starting.
INFO [2019-10-16 05:18:43] Number of unique permutations: 2
INFO [2019-10-16 05:18:43] Getting ranking at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr1 : mGSZ finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr1 : IGSA analysis ended.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] Starting MIGSA analysis.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:43] 10 Gene Sets.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : dEnricher starting.
INFO [2019-10-16 05:18:43] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:43] Using user provided BR: 1000 genes.
INFO [2019-10-16 05:18:43] Running SEA at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : dEnricher finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : mGSZ starting.
INFO [2019-10-16 05:18:43] Number of unique permutations: 2
INFO [2019-10-16 05:18:43] Getting ranking at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : mGSZ finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbr2 : IGSA analysis ended.
INFO [2019-10-16 05:18:43] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] Starting MIGSA analysis.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:43] 10 Gene Sets.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData1 : dEnricher starting.
INFO [2019-10-16 05:18:43] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:43] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:43] Running SEA at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData1 : dEnricher finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData1 : IGSA analysis ended.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] Starting MIGSA analysis.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:43] 10 Gene Sets.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData2 : dEnricher starting.
INFO [2019-10-16 05:18:43] DE genes 9
INFO [2019-10-16 05:18:43] Using user provided BR: 200 genes.
INFO [2019-10-16 05:18:43] Running SEA at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData2 : dEnricher finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_useOwnbrNoExprData2 : IGSA analysis ended.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] Starting MIGSA analysis.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : Starting IGSA analysis.
INFO [2019-10-16 05:18:43] 10 Gene Sets.
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : dEnricher starting.
INFO [2019-10-16 05:18:43] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:43] Using BRIII: 200 genes.
INFO [2019-10-16 05:18:43] Running SEA at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : dEnricher finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : mGSZ starting.
INFO [2019-10-16 05:18:43] Number of unique permutations: 2
INFO [2019-10-16 05:18:43] Getting ranking at cores: 1
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : mGSZ finnished.
INFO [2019-10-16 05:18:43] MIGSA_ok_usebri1 : IGSA analysis ended.
INFO [2019-10-16 05:18:43] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : Starting IGSA analysis.
INFO [2019-10-16 05:18:44] 10 Gene Sets.
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : dEnricher starting.
INFO [2019-10-16 05:18:44] DE genes 9 of a total of 200 ( 4.5 %)
INFO [2019-10-16 05:18:44] Using BRI: 100 genes.
INFO [2019-10-16 05:18:44] Running SEA at cores: 1
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : dEnricher finnished.
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : mGSZ starting.
INFO [2019-10-16 05:18:44] Number of unique permutations: 2
INFO [2019-10-16 05:18:44] Getting ranking at cores: 1
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : mGSZ finnished.
INFO [2019-10-16 05:18:44] MIGSA_ok_usebri2 : IGSA analysis ended.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] MIGSA_ok_wrongbrOption : Starting IGSA analysis.
INFO [2019-10-16 05:18:44] 10 Gene Sets.
INFO [2019-10-16 05:18:44] MIGSA_ok_wrongbrOption : dEnricher starting.
INFO [2019-10-16 05:18:44] DE genes 9 of a total of 200 ( 4.5 %)
Error in DEnricher(seaParams(igsaInput), expr_data, fit_options, merged_gene_sets) :
Incorrect br option.
In addition: Warning messages:
1: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
2: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
3: In runDEnricher(dif, gene_sets, br, test = test) :
There are no differentialy expressed genes being used.
WARN [2019-10-16 05:18:44] 1 experiments had errors
WARN [2019-10-16 05:18:44] MIGSA_ok_wrongbrOption had errors
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] MIGSA_wrong_noGSets : Starting IGSA analysis.
Error in IGSA(igsaInput) : No gene sets provided.
WARN [2019-10-16 05:18:44] 1 experiments had errors
WARN [2019-10-16 05:18:44] MIGSA_wrong_noGSets had errors
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] *************************************
INFO [2019-10-16 05:18:44] Starting MIGSA analysis.
INFO [2019-10-16 05:18:44] Number of unique permutations: 6
INFO [2019-10-16 05:18:44] Getting ranking at cores: 1
INFO [2019-10-16 05:18:45] Gene sets enriched in 0 experiments: 186
INFO [2019-10-16 05:18:45] Gene sets enriched in 1 experiments: 14
id Name GS_Name igsaInput1 igsaInput2
1 set1 myGeneSets 0.9914680853 0.4168966300
2 set10 myGeneSets 0.2077634588 0.7604938133
3 set100 myGeneSets 0.6524399615 0.2636081104
4 set101 myGeneSets 0.6028661233 0.7819407689
5 set102 myGeneSets 0.2075885961 0.8634517316
6 set103 myGeneSets 0.9675421042 0.6434408170
7 set104 myGeneSets 0.9849658621 0.8785750164
8 set105 myGeneSets 0.7278610208 0.6978651389
9 set106 myGeneSets 0.0976892057 0.0968769667
10 set107 myGeneSets 0.2721506900 0.2636081104
11 set108 myGeneSets 0.3991092243 0.9495912592
12 set109 myGeneSets 0.0012578955 0.1343382494
13 set11 myGeneSets 0.2325245221 0.1220288916
14 set110 myGeneSets 0.6646992155 0.0048841759
15 set111 myGeneSets 0.2766796796 0.0285823191
16 set112 myGeneSets 0.6660154454 0.2636081104
17 set113 myGeneSets 0.4400743046 0.7241909782
18 set114 myGeneSets 0.9397402270 0.7346948547
19 set115 myGeneSets 0.2325245221 0.2002922056
20 set116 myGeneSets 0.0004180150 0.8727164292
21 set117 myGeneSets 0.4744175398 0.6423134692
22 set118 myGeneSets 0.6519093256 0.2636081104
23 set119 myGeneSets 0.6185708274 0.1293207416
24 set12 myGeneSets 0.8550929366 0.8536352844
25 set120 myGeneSets 0.3793668855 0.3919750079
26 set121 myGeneSets 0.8931401447 0.1034908565
27 set122 myGeneSets 0.9116149136 0.1903054796
28 set123 myGeneSets 0.0508873429 0.0103128205
29 set124 myGeneSets 0.1833337390 0.2283248086
30 set125 myGeneSets 0.7799284054 0.7481653705
31 set126 myGeneSets 0.4429773329 0.8944594825
32 set127 myGeneSets 0.2378326042 0.2973873962
33 set128 myGeneSets 0.8263980501 0.2344423956
34 set129 myGeneSets 0.0191149083 0.3980301604
35 set13 myGeneSets 0.0671403617 0.1812969067
36 set130 myGeneSets 0.9164398103 0.0337251063
37 set131 myGeneSets 0.7505594526 0.2636081104
38 set132 myGeneSets 0.4410521136 0.0617017284
39 set133 myGeneSets 0.3088933371 0.2433263286
40 set134 myGeneSets 0.0747698640 0.3825203010
41 set135 myGeneSets 0.8926505529 0.6776995008
42 set136 myGeneSets 0.1133099383 0.1093459212
43 set137 myGeneSets 0.0257435644 0.1156289328
44 set138 myGeneSets 0.3506069480 0.4360583151
45 set139 myGeneSets 0.1533377996 0.2118871268
46 set14 myGeneSets 0.1188460709 0.5998744759
47 set140 myGeneSets 0.9327233023 0.7782038257
48 set141 myGeneSets 0.9034092737 0.0025403537
49 set142 myGeneSets 0.3139527474 0.0765378155
50 set143 myGeneSets 0.8845664673 0.2636081104
51 set144 myGeneSets 0.3395232735 0.0848710227
52 set145 myGeneSets 0.6478460166 0.1627288229
53 set146 myGeneSets 0.6769878191 0.0070242334
54 set147 myGeneSets 0.8995076570 0.7562516206
55 set148 myGeneSets 0.1373644318 0.8478977499
56 set149 myGeneSets 0.2587133577 0.0008152734
57 set15 myGeneSets 0.6199859807 0.1505221563
58 set150 myGeneSets 0.9969071636 0.3127243231
59 set151 myGeneSets 0.0306639402 0.1385596555
60 set152 myGeneSets 0.1080089918 0.6612838585
61 set153 myGeneSets 0.2325245221 0.8383027804
62 set154 myGeneSets 0.0844954775 0.1133601701
63 set155 myGeneSets 0.7311495820 0.9710670707
64 set156 myGeneSets 0.2325245221 0.6439016956
65 set157 myGeneSets 0.7028765964 0.7849739488
66 set158 myGeneSets 0.9036459359 0.6381604709
67 set159 myGeneSets 0.0182549109 0.3162486650
68 set16 myGeneSets 0.9441334365 0.0625846850
69 set160 myGeneSets 0.4686467331 0.9147440611
70 set161 myGeneSets 0.1331100595 0.0828723811
71 set162 myGeneSets 0.2489373481 0.0324472931
72 set163 myGeneSets 0.0532882047 0.5650531784
73 set164 myGeneSets 0.6976060057 0.5437606734
74 set165 myGeneSets 0.1701308457 0.3786395275
75 set166 myGeneSets 0.7049160548 0.1935983950
76 set167 myGeneSets 0.5354376389 0.6149344293
77 set168 myGeneSets 0.1553155521 0.7877357584
78 set169 myGeneSets 0.9682384817 0.2821725706
79 set17 myGeneSets 0.2357392613 0.5915612490
80 set170 myGeneSets 0.1800025505 0.7196690468
81 set171 myGeneSets 0.0652899683 0.1234583372
82 set172 myGeneSets 0.1541809580 0.3060607994
83 set173 myGeneSets 0.1938456751 0.5649862770
84 set174 myGeneSets 0.1686407456 0.0315782160
85 set175 myGeneSets 0.0846562856 0.1188518691
86 set176 myGeneSets 0.0026571347 0.9761734821
87 set177 myGeneSets 0.6223420232 0.9426735363
88 set178 myGeneSets 0.8792629190 0.1543905536
89 set179 myGeneSets 0.6747578830 0.1144618508
90 set18 myGeneSets 0.6972242878 0.8949072050
91 set180 myGeneSets 0.6609210072 0.8856232213
92 set181 myGeneSets 0.4844967802 0.8729520480
93 set182 myGeneSets 0.1828937162 0.9945898436
94 set183 myGeneSets 0.2325245221 0.3915162900
95 set184 myGeneSets 0.2350732418 0.0945041618
96 set185 myGeneSets 0.0306561987 0.7161333091
97 set186 myGeneSets 0.8299379225 0.0211508927
98 set187 myGeneSets 0.3633989897 0.2636081104
99 set188 myGeneSets 0.2325245221 0.0025403537
100 set189 myGeneSets 0.4351394588 0.0259416309
101 set19 myGeneSets 0.0806036145 0.0807907043
102 set190 myGeneSets 0.2325245221 0.0767486650
103 set191 myGeneSets 0.7413785584 0.6159433083
104 set192 myGeneSets 0.4037529765 0.1648618781
105 set193 myGeneSets 0.7275129252 0.0597811570
106 set194 myGeneSets 0.8599101661 0.0382544043
107 set195 myGeneSets 0.8726950894 0.8217773455
108 set196 myGeneSets 0.5779079861 0.6236190306
109 set197 myGeneSets 0.0072944335 0.2636081104
110 set198 myGeneSets 0.1673099916 0.0337251063
111 set199 myGeneSets 0.2325245221 0.2636081104
112 set2 myGeneSets 0.9467453016 0.0204620793
113 set20 myGeneSets 0.3674051026 0.8993025670
114 set200 myGeneSets 0.0004774665 0.9172041181
115 set21 myGeneSets 0.8201901985 0.4729573991
116 set22 myGeneSets 0.1115516769 0.2636081104
117 set23 myGeneSets 0.9149239934 0.6801083548
118 set24 myGeneSets 0.8552306435 0.3999973051
119 set25 myGeneSets 0.6726173944 0.1726171015
120 set26 myGeneSets 0.3389275559 0.2019972225
121 set27 myGeneSets 0.9743070454 0.1341676161
122 set28 myGeneSets 0.6029492827 0.1893462049
123 set29 myGeneSets 0.2100309165 0.4175269585
124 set3 myGeneSets 0.3879637562 0.0072158580
125 set30 myGeneSets 0.2325245221 0.0509307325
126 set31 myGeneSets 0.3875964808 0.0480790484
127 set32 myGeneSets 0.2468863267 0.5482852513
128 set33 myGeneSets 0.0263061255 0.0038030260
129 set34 myGeneSets 0.0755101086 0.6999320946
130 set35 myGeneSets 0.3663517537 0.1668681380
131 set36 myGeneSets 0.2325245221 0.0337251063
132 set37 myGeneSets 0.0016619311 0.2636081104
133 set38 myGeneSets 0.8489631930 0.4084607480
134 set39 myGeneSets 0.5522477107 0.7391784048
135 set4 myGeneSets 0.9335442444 0.2636081104
136 set40 myGeneSets 0.2325245221 0.2636081104
137 set41 myGeneSets 0.4763762069 0.2254261790
138 set42 myGeneSets 0.0126301418 0.6930395372
139 set43 myGeneSets 0.3798400922 0.1266492135
140 set44 myGeneSets 0.2325245221 0.1394188193
141 set45 myGeneSets 0.6620019985 0.0890050925
142 set46 myGeneSets 0.2325245221 0.9426411416
143 set47 myGeneSets 0.1124578652 0.9816946638
144 set48 myGeneSets 0.8425070349 0.2053180739
145 set49 myGeneSets 0.8632151812 0.7314909064
146 set5 myGeneSets 0.0818141664 0.3818603552
147 set50 myGeneSets 0.9215449879 0.8590358443
148 set51 myGeneSets 0.6362625813 0.6121783056
149 set52 myGeneSets 0.5467404688 0.8410637728
150 set53 myGeneSets 0.4499763142 0.8026402330
151 set54 myGeneSets 0.2325245221 0.7176210502
152 set55 myGeneSets 0.0778172813 0.1488708302
153 set56 myGeneSets 0.6932611585 0.0098365760
154 set57 myGeneSets 0.3412720183 0.7787995350
155 set58 myGeneSets 0.9148574195 0.2636081104
156 set59 myGeneSets 0.1554817168 0.2075876600
157 set6 myGeneSets 0.8288302160 0.4269604520
158 set60 myGeneSets 0.7004109327 0.7009680745
159 set61 myGeneSets 0.0257435644 0.2636081104
160 set62 myGeneSets 0.5594080390 0.2636081104
161 set63 myGeneSets 0.3544279599 0.2636081104
162 set64 myGeneSets 0.4659211160 0.6806334019
163 set65 myGeneSets 0.7703370283 0.2678343420
164 set66 myGeneSets 0.8455749956 0.6833387245
165 set67 myGeneSets 0.6351691930 0.9293771610
166 set68 myGeneSets 0.8873273715 0.1642212629
167 set69 myGeneSets 0.6586275711 0.2405258305
168 set7 myGeneSets 0.2625428482 0.2636081104
169 set70 myGeneSets 0.2325245221 0.5931253640
170 set71 myGeneSets 0.0878540376 0.0232157689
171 set72 myGeneSets 0.1741649934 0.1849660763
172 set73 myGeneSets 0.7633023538 0.9416729567
173 set74 myGeneSets 0.0867563437 0.2636081104
174 set75 myGeneSets 0.8709992962 0.0858845718
175 set76 myGeneSets 0.2325245221 0.4750379273
176 set77 myGeneSets 0.0984344452 0.3778709683
177 set78 myGeneSets 0.8630192935 0.0424942618
178 set79 myGeneSets 0.8933633628 0.2604480883
179 set8 myGeneSets 0.2325245221 0.3543968025
180 set80 myGeneSets 0.9775811773 0.0337251063
181 set81 myGeneSets 0.0179728884 0.3842944699
182 set82 myGeneSets 0.1373931570 0.6549650313
183 set83 myGeneSets 0.2325245221 0.1491929017
184 set84 myGeneSets 0.2810828326 0.2099679276
185 set85 myGeneSets 0.2928053872 0.2636081104
186 set86 myGeneSets 0.9670592552 0.1298954445
187 set87 myGeneSets 0.3556141919 0.9408833834
188 set88 myGeneSets 0.7661234566 0.2531155642
189 set89 myGeneSets 0.8533546654 0.3701744384
190 set9 myGeneSets 0.2631788445 0.4256747832
191 set90 myGeneSets 0.7219530942 0.9620316887
192 set91 myGeneSets 0.0883950480 0.5610455932
193 set92 myGeneSets 0.7898776660 0.1922651204
194 set93 myGeneSets 0.1376995687 0.1111976766
195 set94 myGeneSets 0.6926679462 0.9141710458
196 set95 myGeneSets 0.2325245221 0.0529390033
197 set96 myGeneSets 0.1525256696 0.4954544930
198 set97 myGeneSets 0.8118502439 0.7513042427
199 set98 myGeneSets 0.5386436490 0.8443455662
200 set99 myGeneSets 0.5017492400 0.1614411097
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
RUNIT TEST PROTOCOL -- Wed Oct 16 05:18:55 2019
***********************************************
Number of test functions: 87
Number of errors: 0
Number of failures: 0
1 Test Suite :
MIGSA RUnit Tests - 87 test functions, 0 errors, 0 failures
Number of test functions: 87
Number of errors: 0
Number of failures: 0
Warning messages:
1: In filterByGenes(migsaRes, "") :
Provided genes did not contribute to enrich any gene set.
2: In filterByGenes(migsaRes, c("fakeGene1", "fakeGene2")) :
Provided genes did not contribute to enrich any gene set.
3: In filterByGenes(migsaRes, impGenes) :
No enriched gene set with used cutOff.
4: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
5: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
6: In setDefaultEnrCutoff(migsaRes) : No enrichment cutoff set. Using 0.01
>
> proc.time()
user system elapsed
31.10 1.79 32.67
|
