SWATH2stats 1.2.3
Peter Blattmann
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/SWATH2stats | | Last Changed Rev: 117776 / Revision: 122332 | | Last Changed Date: 2016-05-23 08:18:35 -0700 (Mon, 23 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r SWATH2stats -R && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SWATH2stats
###
##############################################################################
##############################################################################
* checking for file 'SWATH2stats/DESCRIPTION' ... OK
* preparing 'SWATH2stats':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"E:/biocbld/bbs-3.3-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Number of non-decoy peptides: 262
Number of decoy peptides: 11
Decoy rate: 0.0420
assess_fdr_overall_testrun.pdf written to working folder
assess_fdr_overall_testruntable.csv written to working folder
The average FDR by run on assay level is 0.003
The average FDR by run on peptide level is 0.004
The average FDR by run on protein level is 0.078
Individual run FDR qualities can be retrieved from assess_fdr_byrun_testrun .csv
assess_fdr_byrun_testrun.csv reports written to working folder
assess_fdr_byrun_testrun.pdf report plots written to working folder
The average FDR by run on assay level is 0.003
The average FDR by run on peptide level is 0.004
The average FDR by run on protein level is 0.078
Target assay FDR: 0.01
Required overall m-score cutoff:0.01
achieving assay FDR =0.0066
Target peptide FDR:0.02
Required overall m-score cutoff:0.01
achieving peptide FDR =0.00905
Target protein FDR:0.02
Required overall m-score cutoff:0.00017783
achieving protein FDR =0
Dimension difference: 915, 0
Treshold, peptides need to have been quantified in more conditions than: 4.8
Fraction of peptides selected: 0.39
Dimension difference: 1361, 0
filter_mscore_fdr is filtering the data...
-------------------------------------------------------------
finding m-score cutoff to achieve desired protein FDR in protein master list..
Target protein FDR:0.03
Required overall m-score cutoff:0.00017783
achieving protein FDR =0
finding m-score cutoff to achieve desired global peptide FDR..
Target peptide FDR:0.05
Required overall m-score cutoff:0.01
achieving peptide FDR =0.00905
The average FDR by run on assay level is 0.003
The average FDR by run on peptide level is 0.004
The average FDR by run on protein level is 0.078
-------------------------------------------------------------
Proteins selected:
Total proteins selected: 9
Thereof target proteins: 9
Thereof decoy proteins: 0
Peptides mapping to these protein entries selected:
Total mapping peptides: 232
Thereof target peptides: 232
Thereof decoy peptides: 0
Total peptides selected from:
Total peptides: 235
Thereof target peptides: 235
Thereof decoy peptides: 0
-------------------------------------------------------------
Individual run FDR quality of the peptides selected from:
NA
-----------------------------------------------------------
The decoys have been removed from the returned data
Number of proteins detected: 10
Protein identifiers: Protein6, Protein1, Protein7, Protein8, Protein2, Protein4
Number of proteins detected that are supported by a proteotypic peptide: 8
Number of proteotypic peptides detected: 121
Number of proteins detected: 10
Protein identifiers: Protein6Protein1Protein7Protein8Protein2Protein4
Before filtering:
Number of proteins: 9
Number of peptides: 123
Percentage of peptides removed: 70.73%
After filtering:
Number of proteins: 9
Number of peptides: 36
Before filtering:
Number of proteins: 9
Number of peptides: 36
Percentage of peptides removed: 2.78%
After filtering:
Number of proteins: 8
Number of peptides: 35
The library contains 6 transitions per precursor.
The data table was transformed into a table containing one row per transition.
One or several columns required by MSstats were not in the data.
Missing columns: ProductCharge, IsotopeLabelType
IsotopeLabelType was filled with light.
Warning in convert4MSstats(data.transition) :
Intensity values that were 0, were replaced by NA
Error: processing vignette 'SWATH2stats_vignette.Rnw' failed with diagnostics:
chunk 37
Error in library(MSstats) : there is no package called 'MSstats'
Execution halted