[BioC] P calls (VSN and RMA)

[Rafael A. Irizarry]

i agree with wolfgang. to reiterate, what is very important is that you
remember that due to uncertainity in measurement (not to mention Naef's
observation), there is also
uncertainty in P/A calls and any other filtering operation. what is
lacking is a rigorous assssment of this uncertainty. 
thus, by filtering genes before looking
at other stats (such as fold change) you will likely introduce false
negatives but wont have a clue of how much. i havent seen evidence
suggesting that, when using RMA, this
sacrifice in sensitivity is worth the gain in specificity. although, for
MAS 5.0 it certailiny helps.

another issue is how do you define P/A when you get differing calls in
technical (or biological) replicates. i have seen many arbitrary choices
used such as requiring 80% presence... but again, i havent seen evidence
suggesting this helps, when using RMA.


On Fri, 9 Jan 2004 w.huber at dkfz-heidelberg.de wrote:

> 
> > ... 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
> 
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