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:

 

15032 Hunter Court

Westfield, IN  46074

 

(317) 490-5129 Work, & Mobile

 

(317) 663-0513 Home (no voice mail please)

1-(317)-536-2730 FAX


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