[BioC] fold change after gcrma()

Benilton Carvalho beniltoncarvalho at gmail.com
Mon Jun 13 15:58:54 CEST 2011

take a look on chapter 11 of the limma user guide... there is one
example with rma, which you will replace by gcrma on your example. b

On 13 June 2011 14:46, yotsawat pomyen <yotsa at yahoo.com> wrote:
> Dear All,
> I normalised and summarised my data using gcrma() routine and have the
> expression values for each probeset. I now want to do the comparison between two
> classes of the samples (i.e. fold change between the classes). One thing I'm not
> sure is how to compare them because, as I read from the gcrma paper, the
> expression values after the gcrma() routine are log(intensity) after background
> adjustment.
> My question is: Do I have to convert the expression values from gcrma() back to
> raw values by e^(values) before calculate the fold change between the two
> classes that I have?
> Best
> Yot
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