## ----------------------------------------------------------------------------- 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