Hi all,
I'm currently interpreting microarray data that has been converted to a gene expression data matrix using the justRMA command. I understand that the data has been log transformed but I just want to check if anyone knows what log base was used for this transformation? I think I remember reading at one point that it was Log2, but I just want to double check.
Huaping Liu
yes，it was log2. If you wanna the raw expression values ，you should log back.
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Kavitha Kannan
yes ,after rma get log 2
we could choose many other ways to preprocess the data, such as RMA (which outputs log2-transformed expression values)
eset.rma = justRMA()
or GCRMA (which also outputs log2-transformed expression values)
library(gcrma)
eset.gcrma = justGCRMA()
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