[BioC] Time course experiment....

Gordon Smyth smyth at wehi.edu.au
Tue Jan 3 02:00:29 CET 2006

topTable() doesn't have a facility for sorting on or presenting the 
F-statistics, because it is individual coefficient orientated.

I have toyed with the idea that perhaps topTable() should output a 
table based on the F-statistic when the argument 'coefficient' is set 
to NULL. In other words topTable() would give individual coef 
significance when a coef is specified, otherwise it would give 
overall significance. Would you find that a useful facility?

Best wishes

At 09:04 AM 3/01/2006, Naomi Altman wrote:
>I did not get the original posting, but doesn't Sohail just need 
>"TopTable" for this?
>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
>> >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
>> >Genome Research Center
>> >500 Sunnyside Boulevard
>> >Woodbury, NY 11797
>> >(516)422-4076
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>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

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