[BioC] mapping gene name to affy id

Robert Gentleman rgentlem at fhcrc.org
Mon Dec 8 01:12:17 CET 2008

is there some reason to not just use the mappings provided?

> library(hgu133plus2.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Loading required package: tools

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r1Loading required package: DBI
 > r1 = revmap(hgu133plus2SYMBOL)
> r1$"CD86"
[1] "205685_at"   "205686_s_at" "210895_s_at"

biomaRt is great, but why haul things across the internet  you have on the local
file system?

best wishes

Ruppert Valentino wrote:
> Hello,
> I wonder if anyone has come across the same problem as I am having.
> I am trying to map a gene name i.e HGNC symbol to its corresponding affymetrix probe using R/Bioconductor but I don't seem to be able to do it using biomaRt
> I tried :
> getBM(attributes=c("affy_hg_u133_plus_2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u133_plus_2",values="CD86", mart=mart)
> and other similar code but they don't work
> The previous version of biomaRt that uses getFeature() worked when I use something like this :
> feat = getFeature(symbol = "CD86", type = "affy_hg_u133_plus_2", mart = mart)
> but I just can't seem to get the same to work using getBM which now superceeds getFeature
> has anyone come across the same problem and if so how did they solve it.
> Many thanks.
> Raphael.
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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