[BiO BB] discrepancy between probe sets for same gene in microarray

[Ann Loraine]

Dear Lichun,

This happens quite a lot, but it isn't clear what to do about it.

These probe sets are sometimes called "redundant probe sets" because they
are annotated as targeting the same gene.  If you look at them in the
Integrated Genome Browser (tool for visualizing genes, tiling array data,
probe sets, etc.) you find that they map to different regions near the
three-prime ends of known gene structures. (You can view the probe set
alignments by clicking the links labeled "IGB" that appear on Affy's probe
set level Web pages in the NetAffx Analysis Center section of the Affymetrix
Web site.)

One would like to think that differential readings from redundant probe sets
indicate something interesting - such as regulated alternative 3-prime end
processing. But...you have to be a bit careful, because sometimes the probe
set-to-target gene annotations are imperfect.

For some discussion of all this, see:

Cui & Loraine
http://www.lifesciencessociety.org/CSB2006/toc/223.2006.html
(sorry ... I can't resist citing our paper!)

and to get related articles, follow the "related links" from here:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17369640&query_hl=7&itool=pubmed_docsumu

Best,

Ann

-- 
Ann Loraine
Assistant Professor
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155