[BioC] Biomart query in Web interface Vs. biomaRt package?

[J.J.P.Lebrec at lumc.nl]

Hi,

Using the web based Biomart tool (
http://www.ensembl.org/biomart/martview/ ) in database=Ensembl 46,
dataset=Homo sapiens Genes (NCBI 36), I have manually extracted all
unique genes' 'External Gene ID' using GO pathway GO:0006996 as a
filter. I obtained 1141 unique genes.

I tried to automate the process using the BiomaRt package with the below
query which only yielded 9 unique genes!

> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> getBM(attributes = "external_gene_id", filters = "go", values =
"GO:0006996", mart = human)
   external_gene_id
1             KIF3A
2              HPS3
3              HPS3
4            DTNBP1
5            DTNBP1
6             KIF5C
7             KIF4A
8              HPS1
9              HPS6
10             HPS6
11             HPS6
12            KIF25
13             HPS4
> 
>
> sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=Fr
ench_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

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

other attached packages:
 biomaRt    RCurl      XML 
"1.10.1"  "0.8-0"  "1.9-0" 
>

I thought the two queries to be equivalent, could you please tell me
what I am doing wrong here?

Many thanks in advance,

Jeremie