[BioC] homology package question

Robert Gentleman rgentlem at fhcrc.org
Wed Apr 18 18:24:50 CEST 2007


Looks like a bug - you might want to use Inparanoid - hopefully we will 
move to that some time in the next six months

James MacDonald 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
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org



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