[BioC] Affy chip annotation changes

[Mark Cowley]

Hi Yuan,
what does 244194_at map to in the annotation csv file from netaffx? There may be some discrepancy between the netaffx search engine & the netaffx csv files.

in these situations, I like to convince myself that affy's doing the right thing. Like Jim said, you could investigate further using various R tools listed below, or, if you haven't used those tools before, then for about 10 minutes work, you can align the 25mer probes for each probeset (which you can get from netaffx) to the genome using BLAT at the UCSC genome browser. This will tell you whether the probes will target ADAM22 or not.

HTH
Mark

On 02/11/2010, at 1:42 AM, Yuan Hao wrote:

> Hi Jim and Martin,
> 
> Thank you very much for your reply! I have a feeling that this question is too vague to be answered unless down to the very end of chip design. However, just for you information. I actually checked these two missing probe sets on NetAFFX from the Affymetrix website, and one of them, "244194_at", seems still linking to ADAM22, while another is not any more.
> 
> Regards,
> Yuan
> 
> I actually checked on NetAffx from the affymetrix website for two missed probe sets corresponding to ADAM22. "2
> On 1 Nov 2010, at 14:05, James W. MacDonald wrote:
> 
>> 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
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
>> -- 
>> 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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor