[BioC] advice on absent present filtering needed

[Kimpel, Mark William]

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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