[BioC] Time course experiment....

[Jenny Drnevich]

At 07:12 PM 1/2/2006, Naomi Altman wrote:
>I would like TopTable to print:
>
>p-value
>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.

I concur... it would be helpful to see whether or not p-value adjustment 
had been done in the object created by topTable, rather than having to look 
back to the code when topTable was called (if it's still 
around...).  Furthermore, it is possible to indicate which adjustment has 
been done by the name of the column, e.g. BH.p or BY.p? I understand these 
requests may not be feasible if the resulting object needs to have the same 
number of columns with the same names every time.

A couple of other suggestions for minor improvements on topTable 
functionality: 1) have "ID" be an option for resort.by; 2) have "all" be an 
option (or even the default!) for number. This second request is really me 
just being lazy and not wanting to look up and type in the number of genes, 
or coding it by  out.table <- topTable(fit, number=length(fit$genes[,1]))

Happy New Year!
Jenny




>--Naomi
>
>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
> >Gordon
> >
> >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?
> >>
> >>--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
> >
>
>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
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at uiuc.edu