[BioC] Affymetrix probeset ids to gene symbols

[Thomas Hampton]

getSYMBOL in package annotate is a nice way to handle this.

I found it easier, at least.

Cheers

Tom
On Jul 3, 2008, at 4:31 PM, Peter Robinson wrote:

> Dear all,
>
> I have a list of affymetrix probeset ids from another program and  
> would like to use annaffy to extract the corresponding gene names.  
> I am still something of a novice at R and am probably doing  
> something silly, but found no answer in the package vignette. My  
> script:
>
>
> library(annaffy)
>
> dat <- read.table('sign.txt.cdt',header=T)
> psets<-dat[,3]
> symbols<-aafSymbol(as.character(psets),"moe430b.db")
> s<-as.character(symbols)
>
> I was surprisied that so few of the probeset ids got identified by  
> this script. WHat am I doing wrong?
>
> THanks Peter
> s<-as.character(symbols)
> > s
>  [1] "character(0)"       "character(0)"       "character(0)"
>  [4] "character(0)"       "character(0)"       "character(0)"
>  [7] "character(0)"       "character(0)"       "character(0)"
> [10] "character(0)"       "character(0)"       "character(0)"
> [13] "character(0)"       "character(0)"       "Egr3"
> [16] "character(0)"       "character(0)"       "character(0)"
> [19] "character(0)"       "character(0)"       "character(0)"
> [22] "character(0)"       "character(0)"       "character(0)"
> [25] "Irak2"              "character(0)"       "Coq10b"
> [28] "character(0)"       "BC063749"           "character(0)"
> [31] "4631422O05Rik"      "character(0)"       "Coq10b"
> [34] "character(0)"       "character(0)"       "AI452195"
> [37] "character(0)"       "character(0)"       "character(0)"
> [40] "Mobkl2a"            "character(0)"       "character(0)"
>
> (...snip....)
>
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