[BioC] Time course experiment....

[viritha]

Naomi Altman <naomi at ...> writes:

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

Hi Naomi,
I had a similiar issue and used TopTable but I am getting only first 10 but how 
should I write the code to get selected probesets based on an adjusted p-value 
less than or equal to 0.05.

code:
 design <- model.matrix(~factor(rep(1:2, each=3)))
 fit <- lmFit(eset, design)
 fit2 <- eBayes(fit)
topTable(fit2,coef=2,adjust="BH")

I have 3 control and 3 treated samples.The eset has the probenames and the 
expression matrix.
So my question is how do I get the data of all the probesets which pass this 
criteria?
Thanks,
Viritha

> 
> 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 ...>
> > >Subject: [BioC] Time course experiment....
> > >To: <bioconductor at ...>
> > >
> > >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 ...
> >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
>