[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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