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

[James W. MacDonald]

Hi Gabriel,

On 2/19/2013 7:05 AM, Gabriel Teku [guest] wrote:
> 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?

Yes. If I take the error you got below, and go to the BioC website, 
click on mailing lists, and then paste into the search box, the second 
result from that search is

https://stat.ethz.ch/pipermail/bioconductor/2010-May/033431.html

Which I believe answers your question.

Best,

Jim


>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099