[BioC] accessing affybatch probe set name

Karin Lagesen karin.lagesen at medisin.uio.no
Tue Feb 13 14:45:02 CET 2007


I am working with a custom Affymetrix array. I am now looking for a
way to access the probe names, that is the probe set name plus an
identifier. I have understood that this would be what would be the
atom number in the custom spesification file.

My affybatch object:


> alldata
AffyBatch object
size of arrays=754x754 features (88845 kb)
cdf=E_colia530222N (11378 affyids)
number of samples=20
number of genes=11378
annotation=ecolia530222n
> 

Now if I do probeNames I get this:


> probeNames(alldata)[1:25]
 [1] "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at"
 [5] "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at"
 [9] "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at"
[13] "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at"
[17] "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at" "AFFX-BioB-3_at"
[21] "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at" "AFFX-BioB-5_at"
[25] "AFFX-BioB-5_at"
> 

This is the identifier per probe. These are however not unique. Is
there a way for me to get the actual unique probe id, or should I just
make them unique myself? 

TIA

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at medisin.uio.no
http://folk.uio.no/karinlag



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