Question: Affymetrix Human Exon Array MPS and PS files contain different probeset groups
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gravatar for Susan Wilson
11.7 years ago by
Susan Wilson50
Susan Wilson50 wrote:
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ADD COMMENTlink modified 11.7 years ago by Williams, Alan40 • written 11.7 years ago by Susan Wilson50
Answer: Affymetrix Human Exon Array MPS and PS files contain different probeset groups
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gravatar for Michal Okoniewski
11.7 years ago by
Michal Okoniewski190 wrote:
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] > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >
ADD COMMENTlink written 11.7 years ago by Michal Okoniewski190
Answer: Affymetrix Human Exon Array MPS and PS files contain different probeset groups
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gravatar for Williams, Alan
11.7 years ago by
Williams, Alan40 wrote:
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. Best, We are hiring in informatics: http://www.affymetrix.com/corporate/careers/careers.jsp Alan Williams | Sr. Director, Informatics | Informatics Affymetrix, Inc. | 6550 Vallejo Street, Suite 100 | Emeryville, CA 94608 Tel: 510-428-8513 | Fax: 510-428-8585 | Exec Admin: 408-731-5333 alan_williams at affymetrix.com Michal wrote: >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? ------------------------------------------------------------ This transmission is intended for the sole use of the individual and entity to whom it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. You are hereby notified that any use, dissemination, distribution or duplication of this transmission by someone other than the intended addressee or its designated agent is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by reply to this transmission and delete it from your computer. Thank You. Affymetrix, Inc.
ADD COMMENTlink written 11.7 years ago by Williams, Alan40
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