I am trying to obtain normalized expression values for Affymetrix microarray data that we have using bioconductor. The script I have is mostly there, however, I am irked that the row header describes the samples by the file names of the CEL files, rather than the sample names designated in Targets.txt.

Here is an excerpt of my Targets.txt file:

# file for use by limma and affylmGUI. the targets are per-condition and per-time-point.        
Name    FileName    Target
feh.rep1    FH1.CEL    feh
feh.rep2    FH2.CEL    feh
feh.rep3    FH3.CEL    feh
...

Here is the R script:

library(affy)
library(gcrma)
# phenotype data
pd <- read.AnnotatedDataFrame("Targets.txt", header=T)
affy.data <- ReadAffy(filenames=pd$FileName, phenoData=pd)
# gene expression data, normalized by GCRMA
eset <- gcrma(affy.data)
write.exprs(eset, "cs_hm_feh-expression-gcrma-2011-01-12.tsv", sep="\t", row)

I have tried using

affy.data <- ReadAffy(filenames=pd$FileName, phenoData=pd, sampleNames=row.names(pd))

however, that was unsuccessful. Further investigation shows that row.names isn't actually getting anything at all

> row.names(pd)
NULL

which I find perplexing, given that the object shows it has row names, which are exactly what I want (and expected) as my sample labels in the final CSV table:

> pd
An object of class "AnnotatedDataFrame"
  rowNames: feh.rep1, feh.rep2, ..., cs.8d.rep3  (27 total)
  varLabels and varMetadata description:
    FileName: 
    Target:

Any help is appreciated, as I wield R fairly ignorantly and can not figure my way through this one seemingly simple task.