[BioC] homology package question

[James MacDonald]

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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