[BioC] GCRMA background correction for a subset of genes

[odlc at uchicago.edu]

Hi,

I am analyzing data from a custom affy array that
contains genes from several species, while the
samples come from only one of the species. It seems
reasonable to try the GCRMA background correction
using only the features corresponding to that one
species.

However, the current design of the affybatches
makes it impossible to subset by genes, and the
bg.adjust.gcrma function does not seem to have
an option to use only a subset of the genes.

Any suggestions?

Thank you!

Omar.


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Omar De la Cruz
Department of Statistics
University of Chicago