[BioC] Affy chip annotation changes

[Yuan Hao]

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