Hi All,

Regarding gene filters, is it a good idea to filter out genes, which don't
have any annotation?
For many probesets, we end up with 'Transcribed Locus' or 'EST' or 'cDNA
clone' kind of annotation.  These genes, anyway won't give any information
even if they are selected by a statistical test.

Cheers,
Sharon

On 2/20/06, Jenny Drnevich <drnevich@uiuc.edu> wrote:
>
> Hello all,
>
> I have also pondered over the issue of filtering genes to reduce the
> amount
> of multiple hypothesis correction and what is or isn't valid
> statistically.
> I do routinely filter on some estimate of "presence", either Affy's P/M/A
> calls, or for spotted arrays, comparison to blanks, buffers and/or
> negative
> controls. However, I only filter if a gene is not deemed "present" on all
> of the arrays; my rationale for this is that if it's a whole-genome array,
> only a subset of those genes will be expressed in any particular tissue,
> developmental stage, etc. I keep a gene if it is "present" in at least one
> sample rather than say, half the samples as I've seen in other analyses,
> because the possibility exists that a gene may be expressed in only one of
> the treatment groups.
>
> On the other hand, I've never been comfortable with filtering on even a
> non-specific measure of variation across arrays. After reading's Jim's
> response, I agree that if you're mainly interested in sample
> classification, then it could be reasonable to filter out genes that do
> not
> vary, but it still doesn't seem right to do this if you're mainly
> interested in determining differential expression between two or more
> known
> classes. My reasoning is that the p-values are based on the null
> F-distribution, and that by removing genes with little variance, you are
> in
> effect removing the left side of the F-distribution, which would seem to
> invalidate the p-values because the area under the remaining distribution
> has changed. If you couldn't tell, my logic is not based on formal
> statistical theory but rather on my intuitive feel on the matter!
>
> Cheers,
> Jenny
>
>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich@uiuc.edu
>
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