[BioC] getGene in biomaRt package

[sdurinck]

Hi James,

This is probably due to a change in the VEGA BioMart database and I will
check this out.  You should be able to use Ensembl though to get gene
information from entrezgene identifiers using quotes or not.

Try the following:

> mart=martConnect()
connected to:  ensembl_mart_35

> getGene(id=100, type="entrezgene", species="hsapiens", mart=mart)
   id symbol
1 100    ADA
                                                                       
                 description
1 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase).
[Source:Uniprot/SWISSPROT;Acc:P00813]
    band chromosome    start      end strand          martID
1 q13.12         20 42681578 42713790     -1 ENSG00000196839

> getGene(id="100", type="entrezgene", species="hsapiens", mart=mart)
   id symbol
1 100    ADA
                                                                       
                 description
1 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase).
[Source:Uniprot/SWISSPROT;Acc:P00813]
    band chromosome    start      end strand          martID
1 q13.12         20 42681578 42713790     -1 ENSG00000196839




I get an error when I run the example for getGene in the biomaRt package
on both windows and linux. It appears that the martTable class expects
the id to be character, but for e.g. Entrez Gene the id is numeric. If I
substitute id="100", I get a martTable, but with all NA for all slots
but the id.


>> example(getGene)


getGen> if (interactive()) {
    mart <- martConnect(biomarts = c("ensembl", "vega"))
    g = getGene(id = "1939_at", array = "hg_u95av2", mart = mart)
    show(g)
    g = getGene(id = 100, type = "entrezgene", species = "hsapiens", 
        db = "vega", mar .... [TRUNCATED] 
connected to:  ensembl_mart_35
connected to:  vega_mart_35
An object of class "martTable"
Slot "id":
[1] "1939_at"

Slot "table":
$symbol
[1] "TP53"

$description
[1] "Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein
p53) (Antigen NY-CO-13). [Source:Uniprot/SWISSPROT;Acc:P04637]"

$band
[1] "p13.1"

$chromosome
[1] "17"

$start
[1] 7512464

$end
[1] 7531642

$martID
[1] "ENSG00000141510"


Error in validObject(.Object) : invalid class "martTable" object:
invalid object for slot "id" in class "martTable": got class "numeric",
should be or extend class "character"

>> sessionInfo()

R version 2.2.0, 2005-10-12, i386-pc-mingw32 

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
    "datasets" 
[8] "base"     

other attached packages:
       biomaRt            XML         RMySQL            DBI
hs133phsug6cdf           affy 
       "1.4.0"       "0.97-0"        "0.5-6"        "0.1-9"       
"6.0.0"        "1.8.1" 
       Biobase 
       "1.7.4" 

Any ideas?

Jim




James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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