[BioC] How map probeset_id to gene_symbols or other annotation information?

[Peng Yu]

Hi,

I have run the following 'run.R' script, which generated the file
'gene.txt'. My question is how to map the probeset_ids to the gene
names or other information that is available in
http://www.affymetrix.com/analysis/downloads/na29/wtgene/MoGene-1_0-st-v1.na29.mm9.probeset.csv.zip?
What package I should use to read the '.csv' file?

Regards,
Peng


$cat run.R
library(oligo)
data<-read.celfiles(list.celfiles())
eset<-rma(data)
write.exprs(eset, file="genes.txt", sep="\t")

$ head genes.txt
        koA-mth_HZ_5238_MST1_19389.cel  koB-mth_HZ_5238_MST1_19390.cel
 koC-mth_HZ_5238_MST1_19391.cel  koD-mth_HZ_5238_MST1_19392.cel
wt1-mth_HZ_5238_MST1_19385.cel  wt2-mth_HZ_5238_MST1_19386.cel
wt3-mth_HZ_5238_MST1_19387.cel  wt4-mth_HZ_5238_MST1_19388.cel
10344615        7.07210987006919        7.01089258722033
7.26426270000726.92980486555595 7.72857978063884
6.91124431275741        7.457761829613277.21025349865986
10344617        3.02519545040591        3.08697023169755
3.032032340858283.09846420636071        3.12487891156704
3.10727683101607        3.0544609560487 3.03353963677405
10344619        3.20294677833793        3.20612630466463
3.176553031536723.13210443165341        3.1378507207366
3.21452663497659        3.313450502242243.09287042099817
10344621        4.70984671316916        4.68863215464979
4.437058573307564.59970839525133        4.66911715996711
4.80422412543456        4.57334787499862        4.60736276830484
10344623        7.79927399492793        7.78057650451938
7.727104168704187.68525205462879        7.66271776323834
7.65761154201622        7.67860029345257        7.80684426781102
10344625        8.43869623252839        9.23986002214653
9.014821817262028.8450593076064 8.59194370149885
9.08344656110017        9.074688130046138.92291936928794
10344626        10.0590964382247        9.75778614016683
9.668744583401899.91560261746937        9.97497585580347
9.90593250683953        9.72513220186519        10.0570156812405
10344627        7.45353674141328        7.85528510695415
7.12399388341447.48673272391552 8.2401362665769 7.24092300626232
 7.4348487408975 7.8999935331867
10344628        10.1181530678991        10.2050144957479
10.082132643217510.2014962484731        10.3549307008668
9.97359523972773        9.82152593658235        10.0714458425003