[BioC] hs.Mm.inp.db problem

[Iain Gallagher]

Hi - Just a follow up post.

The title should of course be hom.Mm.inp.db problem and session info is below:

> sessionInfo()
R version 2.9.0 (2009-04-17) 
x86_64-pc-linux-gnu 

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] org.Hs.eg.db_2.2.11  org.Mm.eg.db_2.2.11  hom.Mm.inp.db_2.2.11
[4] RSQLite_0.7-1        DBI_0.2-4            AnnotationDbi_1.6.0 
[7] Biobase_2.4.1       
> 
Thanks

Iain

--- On Thu, 12/11/09, Iain Gallagher <iaingallagher at btopenworld.com> wrote:

> From: Iain Gallagher <iaingallagher at btopenworld.com>
> Subject: [BioC] hs.Mm.inp.db problem
> To: bioconductor at stat.math.ethz.ch
> Date: Thursday, 12 November, 2009, 18:41
> Hello List
> 
> I am trying to map ~5000 mouse genes to human genes using
> the inparanoid package and I am failing miserably!
> 
> Having followed the example in the documentation I can't
> get any of my 5000 mouse genes converted to human EG ids.
> 
> Example follows with 3 genes only:
> 
> rm(list=ls())
> 
> library(hom.Mm.inp.db)
> library(org.Mm.eg.db)
> library(org.Hs.eg.db)
> 
> #mouse genes in as symbols
> dataIn <- c('Ints7', 'Upp1', 'Cdc2a')
> 
> #map these to mouse EG ids
> egIds <- revmap(org.Mm.egSYMBOL)
> mapped <- mappedkeys(egIds)
> egIds <- as.list(egIds[mapped])
> ind <- which(names(egIds)%in%dataIn)
> egIdsIn <- egIds[ind]
> #map these IDs to ENSEMBL protein Ids as used for the
> inparanoid mapping
> mouseProtIds <-
> mget(unlist(egIdsIn),org.Mm.egENSEMBLPROT)
> mouseProtIds <- mouseProtIds[!is.na(mouseProtIds)]
> 
> #this is the point of failure!
> rawHumanProtIds <-
> mget(unlist(mouseProtIds),hom.Mm.inpHOMSA,ifnotfound=NA)
> 
> 
> the returned list is full of NA
> 
> Using biomart on the Ensembl site I can get:
> 
> Ensembl Transcript ID    Human Ensembl Protein
> ID
> ENSMUST00000020099   
>    ENSP00000397973
> 
> For example, for Cdc2a, so I know there are homologs there,
> but for some reason the inparanoid package is not working
> for me.
> Using the example in the documentation it does work though
> so I'm assuming the mistake is with me.
> 
> Can anyone help with this (more curiosity now - I can get
> the data through biomart)?
> 
> Cheers
> 
> Iain
> 
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