[BioC] biomaRt gives only NA output

Goeman, J.J. (MSTAT) J.J.Goeman at lumc.nl
Thu Sep 22 16:09:00 CEST 2005


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? 


> 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":
[1] NA

[1] NA

[1] NA

[1] NA

> mart
An object of class "Mart"
Slot "ensembl":

Slot "vega":

Slot "sequence":

Slot "snp":

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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