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/13
61
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
>
> [[alternative HTML version deleted]]
>
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>
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.
>
