[BioC] Detection calls - non-Affy (was "loged data or not loged")
naomi at stat.psu.edu
Mon Apr 4 03:36:25 CEST 2005
You bring up another problem.
We have discussed a number of times how to handle detection calls for Affy
data. (And we did not reach much conclusion, except to agree that the Affy
p-value was questionable).
But absent calls are also problematic for other arrays. E.g. if the
transcript is absent, the P(FG>BG) should be close to .5 and so the spot
will be flagged about 1/2 the time. But if the transcript is present for
one condition and absent for the other, surely this is highly important -
How are peope handling this?
At 05:07 PM 4/3/2005, Wolfgang Huber wrote:
>> While a couple of fixes have been suggested (e.g. Churchill's work and
>> MAANOVA ) these use transformations that are not as readily understood
>> as logarithms.
>The simplicity of logarithms is somewhat of an illusion, though. There is
>no readily understood interpretation when the true expression of a gene in
>some of the conditions is zero (or close to zero). And there are many
>genes like that!
>The only sane solution that I know of is some form of shrunken log-ratios
>(or "generalized", "moderated", however you call it). Some prefer to do it
>via transformation functions that are different from the logarithm
>function at the lower end, some more through the backdoor by biased
>background estimates (to make sure all the data stay away from zero), by
>but the end result is similar.
>European Bioinformatics Institute
>European Molecular Biology Laboratory
>Cambridge CB10 1SD
>Phone: +44 1223 494642
>Fax: +44 1223 494486
Naomi S. Altman 814-865-3791 (voice)
Bioinformatics Consulting Center
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348 (Statistics)
University Park, PA 16802-2111
More information about the Bioconductor