[BioC] P calls (VSN and RMA)

[w.huber at dkfz-heidelberg.de]

> ... One way is simply using an intensity cut, but this
> seems arbitrary, unless it is genuinely linked to detection ability of
> the technology.  Does anyone have comments or ideas?

Btw, there is a very neat paper by Felix Naef that explains why it can be
that for some probes the MM signal is higher than the PM signal - even if
the gene is expressed and no other interfering transcripts are around.
>From this it follows that a proper interpretation of MMs is rather more
complex than in MAS 5.0 (and I am sure Rafael & Zhijin Wu would have much
more to say about this).

Naef F, Magnasco MO.
Solving the riddle of the bright mismatches: labeling and
effective binding in oligonucleotide arrays.
Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906.
PMID: 12935175

Best wishes
 Wolfgang