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

Williams, Alan Alan_Williams at affymetrix.com
Wed Mar 12 18:43:36 CET 2008

Hi Susan, Michal, and others,

The MPS files have a specific purpose, to indicate which probesets to
use for gene level estimates. We do not include all the probesets for a
gene when computing gene level estimates. Specifically we only include
unique probesets (based on cross hyb predictions) which are not bounded.
Thus while the ps file will include all the probesets associated with
that gene, the mps file will only include those which our software (APT,
Expression Console) uses for computing gene level estimates.


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Michal wrote:
>I have checked the exon probesets for the gene that you mentioned
>with XMAP and exonmap. Probably the first list includes exonic
>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?
>Susan Wilson wrote:
>> Dr. Brewer,
>> I was wondering if you had ever cleared this discrepancy
>>   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? 


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