[BioC] P calls

[w.huber at dkfz-heidelberg.de]

Hi,

> In my opinion an "absent" call just means high values of the MM probes
> compared to their corresponding PM probes; other than that I could not
> detect any difference between genes called "absent" or "present".

And in many cases that could just mean that the "MM" is in a fact a
perfect match for something else (esp. in complex transcriptomes such as
human).  The findings in the paper below seem to confirm that notion.

Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ,
Scherf, U, Speed, TP (2002) Exploration, Normalization, and Summaries of
High Density Oligonucleotide Array Probe Level Data. Accepted for
publication in Biostatistics.
http://biosun01.biostat.jhsph.edu/~ririzarr/papers/index.html


Best regards
Wolfgang Huber