[BioC] Affy: Present calls in an eset

Francois Collin fcollin at sbcglobal.net
Wed Oct 8 12:11:08 MEST 2003

Indeed %present calls is arguably the best of all data quality indicators that are suggested by Affymetrix.  If you rehybe the same hybe mix to chips under different conditions - change scanner, hybridization time or temperature, hybe station - %present calls can vary widely.  Genes don't appear and disappear out of the hybe mix, but probe affinities change under the different conditions.  Making sure that %present calls are consistent across a set of chips is a way to check that the processing and experimental conditions that affect hybridization kinetics were fairly consistent across a set of chips.
As for the Present calls ability to discriminate between samples in which a given mRNA fragment is present vs a samples in which it isn't, it will vary from probe set to probe set.  In an ideal probe sets in which all PM/MM probe pairs have similar non-specific binding affinities and the PM probe has good binding affinity to the target mRNA fragment, and the target doesn't bind to too many other probes on the chip, the calls will work well.  It is not clear for what proportion of probe sets the calls actually work as intended.  You can definitely find probe sets for which MM>>PM for several probe pairs in the set and these fragments will never be called present.  The reverse is also true.  
Very little has been published on the subject as far as I know.  There is the work by Ben Rubenstein mentioned earlier in this thread.  More work obviously need to go into this question.  I think that one should be aware that by screening out absent calls, you may be losing many interesting target fragments.  In the days of MAS 4.0, I recall some genes with negative expression being very good discriminators of tumor class.


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