[BioC] applying coxfilter after LIMMA

James W. MacDonald jmacdon at med.umich.edu
Thu Nov 13 15:01:49 CET 2008

Hi Adrian,

Adrian Johnson wrote:
> Dear group,
> I have two types of samples (cancer and normal) with covariate data
> including survival times.
> I applied limma (and filtered genes that are significantly
> differentially expressed between cancer and normal. Say I have 500
> genes after (adj.P.Value using BH) filtering.
> Is it meaningful to apply coxfilter on those 500 genes (by supplying
> expression values for those 500 genes  and survival times for all
> samples) instead of using kOverA flter.

What is the hypothesis being tested here? A t-test and a Cox model test 
for completely different things, so I don't see why you would follow one 
with the other.


> Thanks
> Ad.
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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