[BioC] Analysis starting from MAS 5.0 txt files

[Björn Usadel]

Hi Maurizio,

using the text files (I guess normalized data?) for downstream anlysis 
works.
Assuming you already took the expression values out of the individual 
files and made one big expression file out of it you can even press the 
data into an exprSet

xx<-read.table("yourdata.txt",sep="\t",header=T,row.names=1)
gh<-new("exprSet",exprs=as.matrix(xx))

You can also just iterate over the files and then get the expression 
values out and bind them together to get to the same result.

But as far as I know you can't unnormalize your data so that RMA is not 
available.

Cheers,
Björn

>Hello,
>
>I have a affymetrix dataset (23 arrays) consisting of txt files from 
>the MAS 5.0 algorithm (original cel files are unavailable). I would 
>like to analyze the data using R and bioconductor, is there any 
>package for starting with these txt files? Also, I would like to do a 
>RMA type normalization, is there anyway to do such a multichip 
>normalization (quantile) on the txt file data?
>
>Maurizio
>
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