[BioC] Invalid fold-filter

[Wittner, Ben, Ph.D.]

Robert,

Could you explain why you say below that filtering on low values is probably a
bad idea in many cases? Also, in what cases do you filter low values and in what
cases not?

I filter out probe-sets for which expression values for two or more classes of
interest are low on the theory that such values are dominated by noise and fold
changes calculated between two such classes are not meaningful.

Thanks.
-Ben

>    You can do non-specific filtering, but all you are really doing there
> is to remove genes that are inherently uninteresting no matter what the
> phenotype of the corresponding sample (if there is no variation in
> expression for a particular gene across samples then it has   no
> information about the phenotype of the sample). Filtering on low values
> is probably a bad idea although many do it (and I used to, and still do
> sometimes depending on the task at hand).
> 
> 
>   Best wishes
>     Robert


------------------------------------------------------
Ben Wittner, 617-643-3166, wittner.ben at mgh.harvard.edu