Thanks, Marc. What you said helps to understand.

I will let you know if I need your help on the code or the updated source.

Di

On Fri, Nov 13, 2009 at 12:33 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi Di,
>
> I can't speak for the origins of the biomaRt homolog information so I
> can only answer half of your question.
>
> The inparanoid packages use data directly from inparanoid.  All of the
> relevant data from inparanoid is included in database for these
> packages.  But only the data that is predicted by this algorithm as
> scoring 100% is used in the actual mapping.  For popular organisms like
> mouse, human and flies, we have made sure to include enough other data
> in the relevant organism packages so that you can patch through the
> appropriate inparanoid packages to retrieve homologs.
>
> Also, inparanoid recently updated their datasources and this was a
> pretty major revision (meaning it unintentionally breaks some things for
> us in terms of updating our inparanoid data).  So if these packages are
> starting to finally get some use please let me know so that I can
> prioritize getting our sources updated to their newer version accordingly.
>
>
>  Marc
>
>
>
> Di Wu wrote:
> > Following up this question, I am trying to get human homolog genes for
> some
> > genes in mouse in Illumin mouse v2 array platform. What is the difference
> in
> > results between using getLDS in biomaRt and the hom.Mm.inp.db package? Do
> > both methods use similar source information?
> >
> > Thanks in advance.
> > Di
> >
> > On Fri, Nov 13, 2009 at 8:28 AM, Iain Gallagher <
> > iaingallagher@btopenworld.com> wrote:
> >
> >
> >> Thanks Mark
> >>
> >> Works a treat.
> >>
> >> Iain
> >>
> >> --- On Thu, 12/11/09, Marc Carlson <mcarlson@fhcrc.org> wrote:
> >>
> >>
> >>> From: Marc Carlson <mcarlson@fhcrc.org>
> >>> Subject: Re: [BioC] hs.Mm.inp.db problem
> >>> To: "Iain Gallagher" <iaingallagher@btopenworld.com>
> >>> Cc: bioconductor@stat.math.ethz.ch
> >>> Date: Thursday, 12 November, 2009, 20:29
> >>> 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@btopenworld.com>
> >>>>
> >>> wrote:
> >>>
> >>>>
> >>>>> From: Iain Gallagher <iaingallagher@btopenworld.com>
> >>>>> Subject: [BioC] hs.Mm.inp.db problem
> >>>>> To: bioconductor@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
> >>>>>
> >>>>> _______________________________________________
> >>>>> Bioconductor mailing list
> >>>>> Bioconductor@stat.math.ethz.ch
> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>>> Search the archives:
> >>>>>
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>>>>
> >>>> _______________________________________________
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> >>>> Search the archives:
> >>>>
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>>>
> >>>
> >> _______________________________________________
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> >>
> >>
> >
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