Re: [R] [BioC] problem with biomaRt getHomolog function

From: Kimpel, Mark William <mkimpel_at_iupui.edu>
Date: Fri 26 Jan 2007 - 16:44:32 GMT

Steffen,

When the new biomaRt tries to load it errors out because I do not have RMySQL installed. There is not a Windows binary for RMySQL and it does contain C code that I do not know how to build.

I do not use the MySQL option in biomaRt. Does RMySQL need to be a required dependency? Below is my screen output and sessionINfo.

require(biomaRt)
Loading required package: biomaRt
Loading required package: RMySQL
Error: package 'RMySQL' could not be loaded In addition: Warning message:
there is no package called 'RMySQL' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
> sessionInfo()

R version 2.5.0 Under development (unstable) (2007-01-19 r40528) 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:
      DBI     limma      affy    affyio   Biobase 
 "0.1-12" "2.9.8" "1.13.14" "1.3.3" "1.13.34"
>

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@mail.nih.gov] Sent: Friday, January 26, 2007 9:24 AM
To: Kimpel, Mark William
Cc: bioconductor@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:
>
>
>
> 15032 Hunter Court
>
> Westfield, IN 46074
>
>
>
> (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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Received on Sat Jan 27 04:22:58 2007

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