[BioC] P calls (VSN and RMA)

[w.huber at dkfz-heidelberg.de]

Hi Isaac and Petra,

On Fri, 9 Jan 2004, Isaac Neuhaus wrote:
> still the biological fact that a lot of the probesets on any chip assay
> genes that are not expressed in the cell type being tested.
> Incorporating the null measurements for these probesets greatly affects
> any kind of multiple test corrections applied in analysis of the data.

The P/A calls from Affymetrix are trying to decide on the presence or
absence of a gene in a single sample. For the kind of statistical analyses
you are talking about, genes that are absent in some samples and present
in others may still be very interesting, maybe the most interesting ones.
On the other hand side, to reduce the multiple testing problem, it is good
to throw out genes that never do anything. However, this is necessarily a
trade-off between false positives and false negatives, and the decision
should, among other things, involve the costs of false positives and false
negatives, respectively. In my opinion, the P/A calls are so popular
mostly because they give a false sense of objectivity and simplicity.
...but, as I said, that's just an opinion.

Best wishes
 Wolfgang



-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber