[BioC] advice on absent present filtering needed

[Naomi Altman]

Your colleague is right.  Surely it is important to know if some 
genes express only in certain phenotypes.  Your method loses this information.

--Naomi


At 10:53 PM 10/25/2006, Kimpel, Mark William wrote:
>I have a question about how to properly apply the MAS5 absent 
>present filtering technique. Within my group, I am advocating 
>setting a cutoff ratio of absent present across phenotypes (i.e. all 
>samples), whereas a colleague is advocating applying the filter 
>within phenotype and passing through the filter any probeset with 
>the A/P ratio of >0.5 within any of the phenotypes (we have 3).
>
>The argument my colleague makes is that some probesets may only be 
>expressed by one phenotype and we want to keep these in, but be 
>stringent within phenotype. This makes some biologic sense, but I am 
>concerned that this filtering within phenotype will introduce bias 
>as low expression levels, as it would seem to, at least in some 
>cases, act like a fold filter at expression levels near the limit of 
>reliable detection.
>
>Advice?
>
>Mark
>
>Mark W. Kimpel MD
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111