[BioC] decideTests with nestedF

James W. MacDonald jmacdon at med.umich.edu
Fri Jun 16 15:01:15 CEST 2006

Hi Pedro,

Pedro López Romero wrote:
> Hi Sean, 
> thanks a lot for the replay. 
> Yes, you understood my doubt. I have several experimental conditions, and I
> thought that filtering first by the moderated F-statistic would be a right
> approach, since by this I would be selecting the genes that are DE in any of
> the contrasts. Now, from this reduced list, I thought that I could select
> the genes for every independent contrast given by my experimental
> conditions. 

I don't think you understand what decideTests() is doing. This function 
fits all the contrasts in your contrasts matrix, using one of several 
different methods. So you cannot use decideTests() to filter your genes 
before doing the contrasts, because decideTests() _is_ doing the contrasts.

As Sean mentioned, if you want to pre-filter your genes, you should be 
filtering using an agnostic approach such as removing those genes that 
have a low variance across all samples.

To answer your original question, I think the problem arises in this 
line of your code:


If this is a direct copy-paste of your code (and not a re-typing), then 
you made a mistake in your p.value argument. It should read 0.05, not 0,05.



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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