[BioC] Affymetrix Human Exon Array MPS and PS files contain different probeset groups

[Michal Okoniewski]

Susan, Daniel,

I have checked the exon probesets for the gene that you mentioned (PTENP1)
with XMAP and exonmap. Probably the first list includes exonic probesets 
known by Affy
at design time, the second exonics and intronics.
See and compare:  http://xmap.picr.man.ac.uk/#10/89623900/15/h
then click the gene name, then click on "Matching Probesets".
So maybe it is not discrepancy, just different annotation...
And why don't you use full annotation, but core, which is just a 
fraction of probesets?

Best,
Michal

Susan Wilson wrote:
> Dr. Brewer,
>
> I was wondering if you had ever cleared this discrepancy https://stat.ethz.ch/pipermail/bioconductor/2007-June/017960.html? 
>   Could it be simply a synchronization problem?  I am an Oracle  
> database person and I have loaded the NetAFFX probeset annotation CSV  
> file into my database and confirm your results (see below).  My  
> inclination is to use the 23 rows version and forget the mps?
>
> $ grep 3256689 HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
> 3256689 3256689 3256702 3256703 3256704 3256705 3256740  
> 3256780         24
>
> vs
>
>
>
> 14:20:07 SQL> l
>    1  select probeset_id from probeset_annot where  
> transcript_cluster_id = '3256689'
>    2* and levelx='core'
> 14:21:06 SQL> /
> 3256702
> 3256703
> 3256704
> 3256705
> 3256706
> 3256707
> 3256708
> 3256709
> 3256710
> 3256711
> 3256725
> 3256736
> 3256738
> 3256739
> 3256740
> 3256764
> 3256767
> 3256772
> 3256773
> 3256777
> 3256778
> 3256779
> 3256780
>
> 23 rows selected.
>
>
> Thanks for your time.
> Susan M. Wilson
>
> Sr. Database Administrator
>      Cancer Research and Treatment Center Shared Resource for
>          Bioinformatics and Computational Biology
>      UNM Center for High Performance Computing
>
> smwilson at hpc.unm.edu [email]
> 505.280.9158 [cell]
> 505.277.2051 [desk]
>
>
>
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