## ------------------------------------------------------------------------
suppressMessages( library( ExpressionAtlas ) )

## ----eval=FALSE----------------------------------------------------------
## atlasRes <- searchAtlasExperiments( properties = "salt", species = "rice" )
## # Searching for Expression Atlas experiments matching your query ...
## # Query successful.
## # Found 3 experiments matching your query.

## ---- echo=FALSE---------------------------------------------------------
data( "atlasRes" )

## ------------------------------------------------------------------------
atlasRes

## ----eval=FALSE----------------------------------------------------------
## allExps <- getAtlasData( atlasRes$Accession )
## # Downloading Expression Atlas experiment summary from:
## #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-GEOD-11175/E-GEOD-11175-atlasExperimentSummary.Rdata
## # Successfully downloaded experiment summary object for E-GEOD-11175
## # Downloading Expression Atlas experiment summary from:
## #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
## # Successfully downloaded experiment summary object for E-MTAB-1625
## # Downloading Expression Atlas experiment summary from:
## #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1624/E-MTAB-1624-atlasExperimentSummary.Rdata
## # Successfully downloaded experiment summary object for E-MTAB-1624

## ---- echo=FALSE---------------------------------------------------------
data( "allExps" )

## ------------------------------------------------------------------------
allExps

## ----eval=FALSE----------------------------------------------------------
## rnaseqExps <- getAtlasData(
##     atlasRes$Accession[
##         grep(
##             "rna-seq",
##             atlasRes$Type,
##             ignore.case = TRUE
##         )
##     ]
## )
## # Downloading Expression Atlas experiment summary from:
## #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-1625/E-MTAB-1625-atlasExperimentSummary.Rdata
## # Successfully downloaded experiment summary object for E-MTAB-1625

## ---- echo=FALSE---------------------------------------------------------
data( "rnaseqExps" )

## ------------------------------------------------------------------------
rnaseqExps

## ------------------------------------------------------------------------
mtab1624 <- allExps[[ "E-MTAB-1624" ]]
mtab1625 <- allExps[[ "E-MTAB-1625" ]]

## ------------------------------------------------------------------------
sumexp <- mtab1625$rnaseq
sumexp

## ------------------------------------------------------------------------
head( assays( sumexp )$counts )

## ------------------------------------------------------------------------
colData( sumexp )

## ------------------------------------------------------------------------
metadata( sumexp )

## ------------------------------------------------------------------------
names( mtab1624 )
affy126data <- mtab1624[[ "A-AFFY-126" ]]
affy126data

## ------------------------------------------------------------------------
head( exprs( affy126data ) )

## ------------------------------------------------------------------------
pData( affy126data )

## ------------------------------------------------------------------------
preproc( experimentData( affy126data ) )

## ----eval=FALSE----------------------------------------------------------
## mtab3007 <- getAtlasExperiment( "E-MTAB-3007" )
## # Downloading Expression Atlas experiment summary from:
## #  ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/atlas/experiments/E-MTAB-3007/E-MTAB-3007-atlasExperimentSummary.Rdata
## # Successfully downloaded experiment summary object for E-MTAB-3007