If this can help,

 outside R you can check "resourcerer" at:

http://compbio.dfci.harvard.edu/tgi/

This allows you to match arrays at probeset level


Marco


On 4/18/07, James MacDonald <jmacdon@med.umich.edu> wrote:
>
> I may be missing something, but I don't understand the contents of the
> mmuhomologyLL2HGID and mmuhomologyHGID2LL environments. My understanding is
> that the former should take an Entrez Gene ID as a key and output a HGID
> number as a value, and the converse for the latter.
>
> I am trying to compare results from an experiment using Human samples to a
> similar experiment using Mouse samples. It seems to me the most reasonable
> way to do this is to map the set of significant genes from one experiment to
> HGIDs and then from HGIDs to Entrez Gene IDs for the second species.
> However, it appears that all the keys for both of these environments are the
> same (and are all Entrez Gene IDs), and the values are all the same (Entrez
> Gene IDs as well). I see this with versions 1.15.13 as well as 1.14.2, for
> both mmuhomology and hsahomology packages.
>
> > get("20863", mmuhomologyHGID2LL)
> 10090
> 20863
> > get("20863", mmuhomologyLL2HGID)
> 10090
> 20863
>
> > all.equal(unlist(as.list(mmuhomologyLL2HGID)),
> unlist(as.list(mmuhomologyHGID2LL)))
> [1] TRUE
>
> Am I missing something? Also, is there a better way to compare the two
> experiments that I am overlooking?
>
> Best,
>
> Jim
>
>
> --
>
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
>
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