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

[Rafael A. Irizarry]

jean wu and i have a manuscript that disucsses some of these issues. if 
interested, you can download it here:

http://www.bepress.com/jhubiostat/paper73/


-r



On Sun, 3 Apr 2005, Naomi Altman wrote:

> 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?
>
> --Naomi
>
> 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
>> England
>> 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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