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.

for the answer to your mas 5 question read this: http://stat- www.berkeley.edu/users/bolstad/MAS5diff/Mas5difference.html 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. On 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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >