Using R2.5.0 and Bioconductor I have been following code to analysis
Affymetrix expression data: 2 treatments vs control.  The original code
was run last year and used the read.phenoData command, however with the
newer version I get the error message
Warning messages:
read.phenoData is deprecated, use read.AnnotatedDataFrame instead
The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
 
I use the read.AnnotatedDataFrame command, but when it comes to the end
of the analysis the comparison of the treatment to the controls gets
mixed up compared to what you get using the original read.phenoData ie
it looks like the 3 groups get labelled wrong and so the comparisons are
different (but they can still be matched up).
My questions are, 
1) do you need to set up your target file differently when using
read.AnnotatedDataFrame - what is the standard format?
I have three columns sample, filename and target.
2) do you need to use a different model matrix to what I have?  
3) do you use a different command for making the contrasts?
I have included my code below if that is of any assistance.
Many Thanks!
Alice
 
 
 
##Read data
pd<-read.AnnotatedDataFrame("targets.txt",header=T,row.name="sample")
Data<-ReadAffy(filenames=pData(pd)$FileName,phenoData=pd)
##normalisation
eset.rma<-rma(Data)
##analysis
targs<-factor(pData(pd)$Target)
design<-model.matrix(~0+targs)
colnames(design)<-levels(targs)
fit<-lmFit(eset.rma,design)
cont.wt<-makeContrasts("treatment1-control","treatment2-control",levels=
design)
fit2<-contrasts.fit(fit,cont.wt)
fit2.eb<-eBayes(fit2)
testconts<-classifyTestsF(fit2.eb,p.value=0.01)
topTable(fit2.eb,coef=2,n=300)
topTable(fit2.eb,coef=1,n=300)
 

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