[BioC] hs.Mm.inp.db problem

[Marc Carlson]

Hi Iain,

The trouble you are having is because inparanoid uses Jackson lab IDs
(MGI) instead of ensembl protein IDs when representing mouse.

So this script should work better:

library(hom.Mm.inp.db)
library(org.Mm.eg.db)
library(org.Hs.eg.db)

dataIn <- c('Ints7', 'Upp1', 'Cdc2a')
egs <- mget(dataIn,revmap(org.Mm.egSYMBOL))

## this is what you want right here:
mouseProtIds <- mget(unlist(egs),org.Mm.egMGI)  
mouseProtIds <- mouseProtIds[!is.na(mouseProtIds)]

rawHumanProtIds <- mget(unlist(mouseProtIds),hom.Mm.inpHOMSA,ifnotfound=NA)

##etc.

Hope this helps,


  Marc



Iain Gallagher wrote:
> 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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>>
>>     
>
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