[BioC] accessing affybatch probe set name

[Kasper Daniel Hansen]

There are no probe ids. Usually one identifies a probe with an (x,y)  
coordinate, which you can get. But note that on some arrays the same  
probe sequence can be spotted at multiple (x,y) locations. The atom  
does not identify a probe, rather a probe-pair (a PM and a MM probe).

Kasper

On Feb 13, 2007, at 5:45 AM, Karin Lagesen wrote:

>
> 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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