[BioC] annotation package: get probenames from gene names

[James W. MacDonald]

Hi Georg,

Georg Otto wrote:
> Hi,
> 
> I need some help with the annotation package:
> 
> To get the gene name for a given probe I perform something like this:
> 
> 
>>zebrafishGENENAME$"Dr.19073.2.S1_a_at"
> 
> [1] "annexin A11a"
> 
> My question is: How can I do it the other way around, i.e. get all
> probes with gene names containing "annexin"?

 > library(zebrafish)
 > tmp <- as.list(zebrafishGENENAME)
 > names(tmp[grep("annexin A11a", tmp)])
[1] "Dr.19073.2.S1_a_at"
 > names(tmp[grep("annexin", tmp)])
  [1] "Dr.19073.2.S1_a_at" "Dr.3457.1.A1_at"    "Dr.4833.1.S1_at" 
"Dr.20555.1.S1_s_at"
  [5] "Dr.20555.1.S2_s_at" "Dr.7658.1.S1_at"    "Dr.11521.1.S1_at" 
"Dr.1190.1.S1_at"
  [9] "Dr.20337.1.S1_at"   "Dr.11764.2.A1_at"   "Dr.20555.1.S1_at" 
"Dr.4833.8.S1_at"
[13] "Dr.1260.1.S1_at"    "Dr.10293.1.S1_at"   "Dr.11764.1.S1_at" 
"Dr.4932.1.S1_at"
[17] "Dr.59.1.S1_at"

HTH,

Jim


> 
> Any hint will be highly appreciated.
> 
> Cheers,
> 
> Georg
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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