Hi Bioconductorians,
 
  In this time ,as reference documentation, i use a web doc: 23. Limma : Linear Models for microarray data ( Of course , written by G.Smith) 
In section 23.11 , Time Course experiments, treated analyse the same way that estrogen data.. but with some difference :
 
Gordon write :" which gene respond at either the 6 h OR 24 h. times in the wt?"
 
code: 
>cont.wt = makeContrasts("wt.6h-wt.0h", "wt.24h-wt.6r", levels =design) 
#build a contraste matrice.
> fit2 = contrasts.fit (fit , cont.wt)
>fit2 = eBayes (fit2)
  
To Choose Interesting Genes
 
sel.wt = p.adjust(fit2$F.p.values, method = "fdr") < 0.05

PROBLEM OF UNDERSTANDING HERE:
in the question "which gene respond at either the 6 h OR 24 h. times in the wt", it's set A OR set B
and to choose interesting genes , there is not distinction between A and B.
 
Hence : May be that the OR ( use here) is inclusive ( Include the AND)  =>  logical OR, by consequently, sel.wt give me the set of DEG  (differential Expressed Genes) at 6 h and 24 h...
 
Am I OK or OutSide.???
 
 
Thamks for your Help..
 
Greg Voisin 
Bioinformatician 
Centre de recherche du CHUM . Montreal
 
 
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