[BioC] Time course experiment....

[Naomi Altman]

I did not get the original posting, but doesn't Sohail just need 
"TopTable" for this?

--Naomi

At 08:51 AM 1/2/2006, Gordon Smyth wrote:
>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111