[BioC] problem with biomaRt getHomolog function
Kimpel, Mark William
mkimpel at iupui.edu
Fri Jan 26 17:26:28 CET 2007
Steffen, never mind, I should have looked first, there is no C code in
your package and it self-extracted just fine.
mark
Mark W. Kimpel MD
(317) 490-5129 Work, & Mobile
(317) 663-0513 Home (no voice mail please)
1-(317)-536-2730 FAX
-----Original Message-----
From: Steffen Durinck [mailto:durincks at mail.nih.gov]
Sent: Friday, January 26, 2007 9:24 AM
To: Kimpel, Mark William
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problem with biomaRt getHomolog function
Hi Mark,
I think the rat entrezgene id 613226 is a recently added entrezgene id
and is not yet available in Ensembl. Ensembl updates every two months
and the last update of entrezgene id 613226 appears to be December 26 of
2006. So this might be the reason.
Also I would suggest you use the developmental version of biomaRt
(biomaRt_1.9.15) to do getHomolog queries. A recent change in the
BioMart suite enables the biomaRt package to retrieve both the id you
use to query and the ids in the result of the query.
Here's an example:
rat.entrezgene.ID=c("24842","83502","24205")
mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl")
rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl")
mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart =
rat.mart,from.type = "entrezgene",to.type="entrezgene",
to.mart=mouse.mart)
> mouse.homolog
V1 V2
1 24842 22059
2 24205 11789
3 24205 NA
4 83502 12550
best,
Steffen
Kimpel, Mark William wrote:
> I am trying to use the getHomolog function of package "biomaRt" to map
> rat entrezgene IDs to mouse entrezgene IDs. For every ID I try, I get
> NULL as return, even when I know that a mouse mapping exists.
>
>
>
> For example, ratID "613226" corresponds to mouse "229706" .
>
>
>
> See my code and sessionInfo below. Anyone know what I am doing wrong?
>
>
>
> Thanks, Mark
>
>
>
>
>> require(DBI)
>>
>
> [1] TRUE
>
>
>> require(biomaRt)
>>
>
> [1] TRUE
>
>
>
>
>> mouse.mart <- useMart("ensembl","mmusculus_gene_ensembl")
>>
>
> Checking attributes and filters ... ok
>
>
>
>
>> rat.mart<- useMart("ensembl", "rnorvegicus_gene_ensembl")
>>
>
> Checking attributes and filters ... ok
>
>
>
>
>> rat.entrezgene.ID<-"613226"
>>
>
>
>>
>>
>
>
>> mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart =
rat.mart,
>>
> from.type = "entrezgene",
>
> + to.type="entrezgene", to.mart=mouse.mart)
>
> Warning message:
>
> getBM returns NULL. in: getHomolog(id = rat.entrezgene.ID, from.mart =
> rat.mart, from.type = "entrezgene",
>
>
>
>
>
>
>> sessionInfo()
>>
>
> R version 2.4.1 (2006-12-18)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] "stats" "graphics" "grDevices" "datasets" "utils"
"tools"
> "methods" "base"
>
>
>
> other attached packages:
>
> biomaRt RCurl XML DBI RWinEdt limma affy
affyio
> Biobase
>
> "1.8.1" "0.8-0" "1.2-0" "0.1-12" "1.7-5" "2.9.1" "1.12.2"
"1.2.0"
> "1.12.2"
>
>
>
> Mark W. Kimpel MD
>
>
>
>
>
> Official Business Address:
>
>
>
> Department of Psychiatry
>
> Indiana University School of Medicine
>
> PR M116
>
> Institute of Psychiatric Research
>
> 791 Union Drive
>
> Indianapolis, IN 46202
>
>
>
> Preferred Mailing Address:
>
>
>
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>
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>
>
>
> (317) 490-5129 Work, & Mobile
>
>
>
> (317) 663-0513 Home (no voice mail please)
>
> 1-(317)-536-2730 FAX
>
>
> [[alternative HTML version deleted]]
>
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--
Steffen Durinck, Ph.D.
Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877
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