[BioC] GEOQuery - MAS5 normalized data

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Fri Nov 7 19:47:09 CET 2008

Dear group / Dear Sean,
I am using GEOQuery to download a MAS5 (U133Plus2 platform) and intend to make it into a expression matrix and compute differential expression between two classes of samples. 

I have downloaded the data into a gse object.  while making a exprSet object using code in vignette:
data.matrix <- log2(do.call("cbind", lapply(GSMList(gse), function(x) {
tab <- Table(x)
 mymatch <- match(probesets, tab$ID_REF)

Should I log2 values from MAS5 'VALUE'("ID_REF","VALUE","DETECTION.P.VALUE")?

since RMA gives log2 values, I am not sure what MAS5 value means. Could someone suggest a way from here. 


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