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@hpc.unm.edu [email]
505.280.9158 [cell]
505.277.2051 [desk]



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