[BioC] MAS on Bioconductor

Rafael A. Irizarry ririzarr at jhsph.edu
Mon Mar 24 14:53:29 MET 2003

for the answer to your mas 5 question read this:


for writing pms to delimeted use the "pm" function to extract the pms 
out of your affybatch, for example:

Data <- ReadAffy()
pms <- pm(Data)

and read the help file on write.table.

Mon, 24 Mar 2003, Kelvin 
Yen wrote:

> 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.
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