I am performing a gene expression analysis and I founded important
differences between the results of the GCRMA normalization obtained in a
Windows machine (gcrma ver.2.16) and a MAC one (gcrma ver.2.18.1). It
consists in a cut off, so all the lower values dissapear. The code is next:

library(affy)
library(gcrma)
affy.data= ReadAffy()
eset.gcrma=justGCRMA() (the same as eset.gcrmax=gcrma(affy.data))

my question is about default values. Does them variate between versions? The
difference is very significant and I tried changing all the arguments, but
not satisfactory results are obtained.

Regards,

  Martín M.

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