[BioC] GOstats on cDNA microarray

[Seth Falcon]

tsoi at musc.edu writes:

> Dear all,
>
> I am trying to study GO enrichment from a cDNA microarray: sheh (human clone)
> from http://www.microarray.org/sfgf/. Currently I am using GOstats 2.0.4, and I
> want to use GOHyperG to find overrepresented GO terms, however, I am not sure
> what to use for the parameter "lib"; if the microarray is Affymetrix, I would
> use the bioconductor package (eg. hgu133plus2) for this parameter, but I am not
> sure
> what to use in my case.

You will need to build an annotation data package using AnnBuilder for
your chip.

You might also be able to use the humanLLMappings package if you are
careful about defining the universe of gene IDs.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org