[BioC] getGene in biomaRt package

[James MacDonald]

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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