How to output a gene expression table using feature data corresponding to certain labels from an ExpressionSet?
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0
Entering edit mode
6.4 years ago
grokaine ▴ 20

Here is what I am doing:

#GDS download and processing test
source("http://bioconductor.org/biocLite.R")
biocLite()
library(GEOquery)
gds <- getGEO('GDS756')
#Convert to ExpressionSet
eset <- GDS2eSet(gds,do.log2=TRUE)

eset is summarized like this:

ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 6 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM21712 GSM21713 ... GSM21718 (6 total)
  varLabels: sample disease.state description
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total)
  fvarLabels: ID Gene title ... GO:Component ID (21 total)
  fvarMetadata: Column labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 16531451 
Annotation: 

What I want is to output a table in a text file, containing the following columns: (Affymetrix probe ID, ENTREZ Gene ID, expression for sample 1, ..., expression for sample n).

Weirdly enough, GEOQuery manual says that eset should not contain annotated genes, but it seems from my basic object inspection that the featureData contains just that. However my R knowledge is limited so I was unable to produce my table from it.

R GEOQuery • 9.7k views
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6
Entering edit mode
6.4 years ago
write.table(data.frame(fData(eset),exprs(eset)),file="expression.txt",row.names=FALSE,sep="\t")
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1
Entering edit mode

Thanks, I modded @Sean Davis line to match my desire output:

feset <- fData(eset)
teset <- exprs(eset)
cnames <- c( c("ID", "GeneID"), colnames(teset))
write.table(data.frame(feset$ID, feset$"Gene ID",teset),file="expression.txt",row.names=FALSE, col.names=cnames, sep="\t")

 

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