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Dear BioC users, sorry to bother you, but I'm new in R/Bioconductor. I' would like to analyze microarray HG-U133A chips as from GSE3494 but using Mas5 as background correction and normalization algorithm. I use the following commands as from library(affy): abatch<- ReadAffy()#to read the cel files eset.mas5 = mas5(abatch)#to run the Mas5 algorithm exprSet.nologs = exprs(eset.mas5)#to get the expression matrix (probesets/genes in rows, chips in columns). exprSet = log(exprSet.nologs, 2)# to transform in log2 the absolute gene expression summarized values. Now the point is: after log2 transformation I found negative values even using a scaling factor of 600. What am I doing wrong? I tried to use the simpleaffy package using justMAS as function and setting a tgt = 600, but the problem still remain. Can anyone help me? thanks in advance Eleonora -- output of sessionInfo(): R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) -- Sent via the guest posting facility at bioconductor.org.