[BioC] GCRMA background correction for a subset of genes

lgautier at altern.org lgautier at altern.org
Wed Nov 28 18:32:30 CET 2007

> 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?

Define your own CDF environment containing only the probes
you want to be used, and associate that environment with
your affybatch.

However beware that with low number of genes, the estimation
of parameters for gcRMA's background correction might be challenged.


> Thank you!
> Omar.
> --
> Omar De la Cruz
> Department of Statistics
> University of Chicago
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