[BioC] biomaRt gives only NA output

[Steffen Durinck]

Hi Jelle,

The problem is that you are using an old version of biomaRt.
Everything will work if you use the biomaRt version 1.2.2 which is 
available from  the developmental packages webpage.

best,
Steffen

Goeman, J.J. (MSTAT) wrote:

> Hi,
>
>I'm trying out the biomaRt package, but I am unable to reproduce the examples in the vignette. I get no error messages, but I do not get the correct output either. The functions getGO, getFeature, getHomolog, getGene, getOMIM and getXref all give empty output (as for getGO below). Only getSNP seems to work correctly. Session info below. 
>
>Does anyone know what could be the matter here? 
>
>Jelle
>
>
>
>  
>
>>library(biomaRt)
>>    
>>
>Loading required package: Biobase
>Loading required package: tools
>Welcome to Bioconductor 
>         Vignettes contain introductory material.  To view, 
>         simply type: openVignette() 
>         For details on reading vignettes, see
>         the openVignette help page.
>Loading required package: RMySQL
>Loading required package: DBI
>Warning message:
>DLL attempted to change FPU control word from 8001f to 9001f 
>  
>
>>mart <- martConnect()
>>    
>>
>-  Connected to: ensembl_mart_33 -
>-  Connected to: vega_mart_33 -
>-  Connected to: snp_mart_33 -
>-  Connected to: sequence_mart_33 -
>  
>
>>getGO(id = "1939_at", array = "hg_u95av2", mart = mart)
>>    
>>
>An object of class "martTable"
>Slot "id":
>[1] "1939_at"
>
>Slot "table":
>$GOID
>[1] NA
>
>$description
>[1] NA
>
>$evidence
>[1] NA
>
>$martID
>[1] NA
>
>
>  
>
>>mart
>>    
>>
>An object of class "Mart"
>Slot "ensembl":
><MySQLConnection:(2608,1)> 
>
>Slot "vega":
><MySQLConnection:(2608,2)> 
>
>Slot "sequence":
><MySQLConnection:(2608,3)> 
>
>Slot "snp":
><MySQLConnection:(2608,4)> 
>
>Slot "arrayToSpecies":
>               V1            V2
>1          canine   cfamiliaris
>2     drosgenome1 dmelanogaster
>3    drosophila_2 dmelanogaster
>4       zebrafish        drerio
>5         chicken       ggallus
>6         hc_g110      hsapiens
>7        hg_focus      hsapiens
>8  hg_u133_plus_2      hsapiens
>9      hg_u133a_2      hsapiens
>10       hg_u133a      hsapiens
>11       hg_u133b      hsapiens
>12      hg_u95av2      hsapiens
>13        hg_u95b      hsapiens
>14        hg_u95c      hsapiens
>15        hg_u95d      hsapiens
>16        hg_u95e      hsapiens
>17       hugenefl      hsapiens
>18       u133_x3p      hsapiens
>19      mg_u74av2     mmusculus
>20      mg_u74bv2     mmusculus
>21      mg_u74cv2     mmusculus
>22     mouse430_2     mmusculus
>23    mouse430a_2     mmusculus
>24       rat230_2   rnorvegicus
>25        rg_u34a   rnorvegicus
>26        rg_u34b   rnorvegicus
>27        rg_u34c   rnorvegicus
>
>  
>
>>sessionInfo()
>>    
>>
>R version 2.1.0, 2005-04-18, i386-pc-mingw32 
>
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
>[7] "datasets"  "base"     
>
>other attached packages:
> biomaRt   RMySQL      DBI  Biobase 
> "1.0.4"  "0.5-6"  "0.1-9" "1.5.12"
>
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>  
>