[BioC] Detection calls - non-Affy (was "loged data or not loged")

Naomi Altman 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 - 
not flagged.

How are peope handling this?


At 05:07 PM 4/3/2005, Wolfgang Huber wrote:
>Hi Naomi,
>>  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.
>Best regards
>   Wolfgang
>Wolfgang Huber
>European Bioinformatics Institute
>European Molecular Biology Laboratory
>Cambridge CB10 1SD
>Phone: +44 1223 494642
>Fax:   +44 1223 494486
>Http:  www.ebi.ac.uk/huber

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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