[BioC] Time course experiment....

[Gordon Smyth]

Dear Sohail,

Well, there are lots of ways to generate such a table. Perhaps the simplest is

   fitsel <- fit2[sel.dif, ]
   as.data.frame( fitsel )

Best wishes
Gordon

>Date: Tue, 20 Dec 2005 14:03:43 -0500
>From: "Khan, Sohail" <khan at cshl.edu>
>Subject: [BioC] Time course experiment....
>To: <bioconductor at stat.math.ethz.ch>
>
>Dear List,
>
>I have performed a time course analysis using limma, as described in 
>"Bioinformatics and Computational Biology Solutions ........".
>How can I get a list of differentially expressed genes?  I've tried 
>the code below:
>sel.dif<-p.adjust(fit2$F.p.vlaue,method="fdr") <0.05
>This produces a logical vector, right?.  I would like a table of 
>differentially expressed genes with p vales etc.  Sorry, if I missed 
>this in the limma user's guide.  Thanks for any suggestions.
>
>
>Sohail Khan
>Scientific Programmer
>COLD SPRING HARBOR LABORATORY
>Genome Research Center
>500 Sunnyside Boulevard
>Woodbury, NY 11797
>(516)422-4076