[BioC] bioMart query

[Natasha Sahgal]

Dear All,

I am trying to annotate my DE gene list using biomart, but keep getting an error and an empty output.
I can't seem to figure out where I have gone wrong in my code (I suspect it might be something really silly).

Help much appreciated. Code below.

##########
library("biomaRt")
listMarts()
listMarts(host='jul2012.archive.ensembl.org'ensembl68 = useMart(host='jul2012.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL')
listDatasets(ensembl68)
ensembl68 = useDataset("hsapiens_gene_ensembl", mart=ensembl68)
listFilters(ensembl68)
listAttributes(ensembl68)

annot.tot = getBM(attributes=c('ensembl_gene_id','external_gene_id','hgnc_symbol','description','entrezgene','chromosome_name','start_position','end_position','strand'),filters='ensembl_gene_id',values= rownames(p12.ip$table),mart=ensembl68)

#####
Warning message:
In getBM(attributes = c("ensembl_gene_id", "external_gene_id", "hgnc_symbol",  :
  Unable to match column names of BioMart output
##########

> head(rownames(p12.ip$table))
[1] "ENSG00000111335" "ENSG00000165949" "ENSG00000187608" "ENSG00000157601"
[5] "ENSG00000119922" "ENSG00000126709"
#####

Many Thanks,
Natasha


SessionInfo:
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.14.0 gdata_2.12.0   WriteXLS_2.2.0 edgeR_2.6.10   limma_3.14.1  

loaded via a namespace (and not attached):
[1] gtools_2.7.0 RCurl_1.95-3 XML_3.95-0.1