[BioC] Help in biomaRt

[Hooiveld, Guido]

Hi Alex,

I had the same problem recently. James MacDonald pointed out that you
have to use the attribute "markersymbol" to retrieve the gene symbol for
a mouse gene (and "hgnc_symbol" when you want to retrieve info on human
genes).

http://thread.gmane.org/gmane.science.biology.informatics.conductor/1361
0

HTH,
Guido
 


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alex Tsoi
> Sent: 18 July 2007 03:57
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Help in biomaRt
> 
> 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.
> 
> 
> --
> Lam C. Tsoi (Alex)
> Medical University of South Carolina
> 
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