Hi Galina,
This was due to a small bug in this function that prevented it from
mapping to mouse IDs. The bug was caused by a change in the inparanoid
mouse annotations and has been fixed in all current versions of
AnnotationDbi (release and devel). You should be able to update
AnnotationDbi in a day or two and benefit from the changes.
Thanks for reporting this,
Marc
On 03/23/2011 02:14 PM, Glazko, Galina V wrote:
> Dear list,
>
> I am trying to translate mouse Entrez ids into human orthologous Entrez ids using inparanoid, and I am getting an error:
>
>> humanEGs<-inpIDMapper(tmp, srcSpecies="MUSMU", destSpecies="HOMSA", srcIDType="EG", destIDType="EG")
> Error in names(destIDs) = dnames : attempt to set an attribute on NULL
>
>> head(tmp)
> [1] "269378" "211660" "211660" "211660" "98711" "669171"
> (looks all right)
>
> I would be grateful if someone could indicate what I am doing wrong.
> Probably I missed something important about the status of INPARANOID database and AnnotationDBI?
>
> In the same time, if I am doing this via BiomaRt:
> tm2<-getLDS(attributes ="entrezgene",filters = "entrezgene", values = tmp, mart = mouse, attributesL = c("affy_hg_u133a","entrezgene"), martL = human)
>
> I get results and at the first glance it looks consistent. But I would prefer to use inparanoid scheme for matching orthologs...
> I would appreciate your help.
>
> Best regards
> Galina
> #------------------------------------------------
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.6.0 hom.Hs.inp.db_2.4.6 org.Hs.eg.db_2.4.6 hom.Mm.inp.db_2.4.6
> [5] mogene10sttranscriptcluster.db_6.0.1 mogene11stprobeset.db_2.0.2 org.Mm.eg.db_2.4.6 RSQLite_0.9-4
> [9] DBI_0.2-5 AnnotationDbi_1.12.0 Biobase_2.10.0 limma_3.6.9
>
>
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