[BioC] Problems with homology packages

[Bosotti, Roberta [Nervianoms]]

Dear Jim,

thanks for your help, it's working now.
I have a further question, once I got the HomologeneIDs, I'd like to get the
Accession numbers for both human and mouse.
The HomologeneIDs that I find do not match with the ones I can retrieve from
the NCBI Homologene home page, possibly because they are based on two
different release. Do you know where I could find HomoloGene and LocusLink
database release that where used in the package?

Thanks again for your kind support,

Roberta

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Monday, July 04, 2005 2:07 PM
To: Bosotti, Roberta [Nervianoms]
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Problems with homology packages


Bosotti, Roberta [Nervianoms] wrote:
> Dear list,
> 
> I'm trying to obtain a list of mouse homologs of human genes present in
> Affymetrix chips (human hgu133plus2 and mouse 430) following the homology
> packages Vignette, but I didn't succeded. Here is the code and the error
> messages I got.
> I'm using R-2.1.1 and Bioconductor 1.6 package.
> Could you help me?
> Thanks, Roberta
> 
> 
>>library("mmuhomology")
>>subset(mmuhomologyORGCODE, species_name == "Homo sapiens")
> 
> Error in subset.matrix(mmuhomologyORGCODE, species_name == "Homo sapiens")
:
> 
>         Object "species_name" not found

What version of the mmuhomology package are you using? This works for me.

 > subset(mmuhomologyORGCODE, species_name =="Homo sapiens")
    species_name tax_id tla
24 Homo sapiens   9606 hsa

> 
>>temp <- mget(mmuhomologyHGID, mmuhomologyDATA)
>>tempFun <- function(x) {
> 
>  for (i in x) {
>  if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
>  "hsa" && i[["homoPS"]] > 90) {
>  return(i)
>  }
>  }
>  return(NA)
>  }
> 

I think you are missing something here. You also have to test for 
homoType == "B". If homoType == "c", then you will return an NA, which 
is why your tempFun is erroring out.

tempFun <- function(x) {

   for (i in x) {
     if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] ==
     "hsa" && i[["homoType"]] == "B" && i[["homoPS"]] > 90) {
     return(i)
     }
   }
   return(NA)
}


HTH,

Jim


>>goodGenes <- sapply(temp, tempFun)> goodGenes <- sapply(temp, tempFun)
> 
> Error in if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "hsa" &&
> i[["homoPS"]] >  : 
>         missing value where TRUE/FALSE needed
> 
> 
> 
> 
>
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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