Dear all,

I encountered the same problem described by monnie McGee using the 
Affycomp library. As adviced by the vignette I've used the "
read.newspikein" function with HG-U133A spikein data.


>library(affy)
>library(affycomp)
>spike133 <- ReadAffy(...)
>eset <- expresso(spike133, bgcorrect.method="rma", 
normalize.method="quantiles", pmcorrect.method="pmonly", 
summary.method="medianpolish")
>new.eset <- exprs(eset)
>write.table(data.frame(new.eset,check.names=FALSE),"rma-133.csv",sep=",",col.names=NA,quote=FALSE)
>read.newspikein("rma-133.csv")
Error in "[.data.frame"(s, , rownames(pData(pd))) :
        undefined columns selected

Any suggestions ?

Thanks

John Brozek

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