[BioC] Affymetrix probeset ids to gene symbols

[Vincent Carey 525-2265]

> 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?

you got some hits so it seems to me that conceptually the solution
is OK.   you do not need to use annaffy for this task.

library(moe430b.db)
mget(psets, moe430bSYMBOL) # or moe430bGENENAME for actual names

would in principle work and would return a little more info

if there are specific elements of psets that you think should map to
names, but don't, state what they are and the symbols that you think
they should resolve to.  also provide a sessionInfo()...

>
> 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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