[BioC] Help in biomaRt

[Wolfgang Huber]

Dear Alex,

can you please please supply the output of "sessionInfo()" with such
reports?

For me, your example code work perfectly well.
Maybe you could benefit from updating to your biomaRt package.

library(biomaRt)
ensembl = useMart("ensembl")
ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)
getGene(id = "98682", type = "entrezgene", mart=ensembl)

  entrezgene  markersymbol
1      98682 2210010L05Rik
2      98682 2210010L05Rik

                                                       description
1 RIKEN cDNA 2210010L05 gene [Source:MarkerSymbol;Acc:MGI:1922925]
2 RIKEN cDNA 2210010L05 gene [Source:MarkerSymbol;Acc:MGI:1922925]

  chromosome_name band strand start_position end_position
1   C1     -1       52601997     52671863
1   C1     -1       52601997     52671863


> sessionInfo()
R version 2.6.0 Under development (unstable) (2007-07-19 r42272)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_1.11.4 RCurl_0.8-1    XML_1.9-0      fortunes_1.3-3

loaded via a namespace (and not attached):
[1] tools_2.6.0


 Best wishes
	Wolfgang




Tsoi ha scritto:
> Dear all,
> 
> I have a list of locus link ID from mouse (eg. 98682, 20336), and would like
> to use biomaRt to retrieve the information (gene symbol, etc.) for each
> locus link ID, here the commands I used:
> 
> 
>> ensembl = useMart("ensembl")
>> ensembl = useDataset("mmusculus_gene_ensembl", mart = ensembl)
> Checking attributes and filters ... ok
>> getGene(id = "98682", type = "entrezgene", mart=ensembl)
> Error in getBM(attributes = c(filter, symbol, "description", chrname,  :
>         Invalid attribute(s): mgi_symbol
> Please use the function 'listAttributes' to get valid attribute names
> 
> 
> I don't have any clue about the error, and I followed the guideline from the
> biomaRt menu.
> 
> I greatly appreciate for any help or suggestion.
> 
> Thanks a lot.
>