[BioC] MAS on Bioconductor

[Kelvin Yen]

Hi,

I'm a new user to Bioconductor and I've been using the Affy package to 
analyze the .Cel files I have.  I tried replicating the analysis I did 
using Affy's MAS program with bioconductor's MAS algorithm but the 
results I get are completely different than the ones I get using the 
original MAS software.  I'm analyzing six .Cel files and using MAS and 
a subsequent t-test on the values, I get many(~30) values that are 
e-05.  But using Bioconductor's MAS algorithm, I only get one.  Here 
are the commands that I'm using to generate the data.

Data <- ReadAffy()
eset <- expresso(Data, normalize=FALSE, bgcorrect.method="mas", 
pmcorrect.method="mas, summary.method="mas")
eset <- affy.scalevalue.exprSet(eset)
write.exprs(eset, file="mas.xls")

I'm using the MGU74aV2 chip.  Any help would be greatly appreciated.

Kelvin Yen
PS I eventually wanted to run the RMA algorithm on my data but first 
wanted to make sure I could replicate data that I already knew the 
value to.