[BioC] Invalid fold-filter

[Sean Davis]

On 2/20/06 8:33, "Bornman, Daniel M" <bornmand at battelle.org> wrote:

> Robert,
> 
> After reading your response to my initial question, I do not believe you
> addressed exactly what I attempted to describe.  Please pardon me for
> not being clear.  I think your response assumed I was filtering on
> unadjusted p-values then applying a correction such as Benjamini &
> Hochberg to a reduced set.
> 
> My question was rather on the validity of first filtering each gene
> based on fold-change between two sample groups (i.e. controls vs
> treated) then calculating a test-statistic, raw p-value and corrected
> p-value on each gene that passed the fold-change filter.  I am worried
> that using the group phenotype description to filter followed by
> applying a p-value correction is unfairly reducing my multiple
> comparison penalty.
> 
> I propose that a less biased approach to fold-filtering would be to
> filter probes based on the mean of the lower half versus the mean of the
> upper half of expression values at each probe regardless of the
> phenotype (non-specific).  This would surely (except in some instances
> where a phenotype causes drastic expression changes) cause the
> fold-filtered set to be larger and thus not unfairly decrease the
> multiple comparison penalty when computing adjusted p-values.

Daniel,

This is routinely done by many folks.  You could use the interquartile
range, the standard deviation, or many others.  As you suggest, such
filtering is done in an unsupervised manner (not using groups).

Sean