[BioC] Affy chip annotation changes

[James W. MacDonald]

Hi Yuan,

The annotation packages we provide are simply a re-packaging of data 
that we get from Affymetrix, so the simple answer is that Affy decided 
that two of those probesets don't really interrogate the transcript for 
that gene.

You could investigate this further by either going to the Affymetrix 
website and downloading the most recent annotation csv file, and the csv 
file that was contemporaneous with the older annotation package 
(2.2.11), and comparing the two. This will likely not be that 
enlightening, as I would bet the annotation simply changes for the two 
probesets that no longer point to ADAM22.

You could also investigate further using e.g., the rtracklayer, 
Biostrings, and BSgenome.Hsapiens.UCSC.hg17 
(BSgenome.Hsapiens.UCSC.hg19) packages.

Best,

Jim



On 11/1/2010 7:14 AM, Yuan Hao wrote:
> Dear list,
>
> I've downloaded two versions of hgu133plus2 array annotation package:
> v2.2.11(R 2.9.2) and v2.4.5 (R 2.12.0). Some probe sets annotated in the
> former version are no longer supported in the recent version. For
> example, "ADAM22" was annotated by eight probe sets ("1555024_at"
> "206615_s_at" "206616_s_at" "208226_x_at" "208227_x_at" "208237_x_at"
> "213411_at" "244194_at"), which have been reduced to six in the latest
> annotation (the last two probe sets have been missing). I would be
> grateful if someone could provide some insight about it, especially for
> this case!
>
> Regards,
> Yuan
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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