R help - Jan 2007 - [BioC] problem with biomaRt getHomolog function

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 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:
>
>  
>
> 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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>   

-- 
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