[BioC] Retrieving dN, dS from biomaRt fails: Attributes from multiple pages not allowed

Gabriel Teku [guest] guest at bioconductor.org
Tue Feb 19 13:05:57 CET 2013


Hi, 

I have EntrezGene IDs for which I want to retrieve dN and dS values from biomaRt.

I've created the mart = "ensembl" for ensembl genes; chosen dataset = "hsapiens_gene_ensembl" for human genes; filter = "entrezgene"; attributes = c("entrezgene"           "mmusculus_homolog_dn" "mmusculus_homolog_ds").

However, when I run getBM() with the above parameters I get the error below.

Any ideas what could be wrong here?

Thanks

Gabriel Teku
Lund University
Faculty of Medicine 
Dept of Experimental Sciences
Protein Structure and Bioinformatics Grp 

 -- output of sessionInfo(): 

> mart = useMart("ensembl")
> mart
Object of class 'Mart':
 Using the ensembl BioMart database
 Using the  dataset
> ensembl <- useDataset(data ="hsapiens_gene_ensembl", mart = ensembl)
> ensembl
Object of class 'Mart':
 Using the ensembl BioMart database
 Using the hsapiens_gene_ensembl dataset
> attrib = listAttributes(ensembl)
> selected.attr <- attrib$name[grepl("(entrezgene|mmusculus_homolog_d)", attrib$name)]
> selected.attr
[1] "entrezgene"           "mmusculus_homolog_dn" "mmusculus_homolog_ds"
> filt = listFilters(ensembl)
> selected.filt <- filt$name[ grepl("^entrezgene", filt$name)]
> selected.filt
[1] "entrezgene"
> head(vs.c05)
[1] "10000" "100"   "10254" "10288" "10392" "10544"
> head(vs.c05) #list of entrezgene ids
[1] "10000" "100"   "10254" "10288" "10392" "10544"
> dn.ds <- getBM(selected.attr, selected.filt, values= vs.c05, ensembl )
Error in getBM(selected.attr, selected.filt, values = vs.c05, ensembl) : 
  Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] biomaRt_2.14.0 seqinr_3.0-7   ape_3.0-7     

loaded via a namespace (and not attached):
[1] gee_4.13-18     grid_2.15.2     lattice_0.20-13 nlme_3.1-108    RCurl_1.95-3    tools_2.15.2    XML_3.95-0.1   

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