[BioC] Time course experiment....

Naomi Altman naomi at stat.psu.edu
Tue Jan 3 02:12:16 CET 2006

I would like TopTable to print:

adjusted "p-value"

using whatever set of p-values is relevant - i.e. either the t-test 
for a coefficient or the F-test for a set of coefficients or the 
overall F-test.


At 08:00 PM 1/2/2006, Gordon Smyth wrote:
>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

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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