Question: problem with fetching gene information in biomaRt for mouse_430_2
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gravatar for oolongoni
12.3 years ago by
oolongoni10
California
oolongoni10 wrote:
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ADD COMMENTlink modified 12.3 years ago by Cei Abreu-Goodger830 • written 12.3 years ago by oolongoni10
Answer: problem with fetching gene information in biomaRt for mouse_430_2
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gravatar for Cei Abreu-Goodger
12.3 years ago by
Mexico
Cei Abreu-Goodger830 wrote:
There are always some discrepancies between different databases. Biomart takes data from Ensembl, which do their own Affy probe-to-genome mapping. The probeset you're looking for isn't mapped to the mouse genome, according to Ensembl. Cei Edmund Chang wrote: > Dear List, > I noticed that for some of the probesets (e.g. 1447625_at), information > retrieved by biomaRt is NULL. However, Affymetrix has it annotated as "E2F5" > when I checked on NetAffx. Why is there a discrepancy? Ultimately, I am > hoping to use biomaRt to find homologs of the mouse probesets on a > Affymetrix human expression array. > Any help in clarifying this situation would be greatly appreciated. Thanks! > > >> library(biomaRt) >> ensembl <- useMart("ensembl") >> mouse <- useMart("ensembl", "mmusculus_gene_ensembl") >> getGene(id="1448859_at", type="affy_mouse430_2", mart =mouse) >> > affy_mouse430_2 markersymbol > 1 1448859_at Cxcl13 > description > chromosome_name band > 1 chemokine (C-X-C motif) ligand 13 > [Source:MarkerSymbol;Acc:MGI:1888499] 5 E3 > strand start_position end_position ensembl_gene_id > ensembl_transcript_id > 1 1 96197241 96201370 ENSMUSG00000023078 > ENSMUST00000023840 > > >> getGene(id="1447625_at", type="affy_mouse430_2", mart =mouse) >> > NULL > > -Ed > Edmund Chang, PhD > One Baylor Plaza M635 > Houston, Tx 77030 > 713-798-6217 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Cei Abreu-Goodger, PhD Wellcome Trust Sanger Institute Computational and Functional Genomics Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD COMMENTlink written 12.3 years ago by Cei Abreu-Goodger830
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