[BioC] toptable with multiple coefs [was Time course experiment....]

[Naomi Altman]

Just as this discussion got underway, I met with my current 
microarray collaborator.

She asked that

a) The results be sorted by gene id
b) all the coefficients and their p-values be printed out to the same 
(big) table
c) all the gene annotations be added to the table

Very timely.

--Naomi


At 07:45 AM 1/3/2006, Sean Davis wrote:



>On 1/3/06 7:40 AM, "Gordon K Smyth" <smyth at wehi.EDU.AU> wrote:
>
> > On Tue, January 3, 2006 11:24 pm, Sean Davis wrote:
> >> On 1/2/06 8:00 PM, "Gordon Smyth" <smyth at wehi.edu.au> 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?
> >>
> >> Gordon,
> >>
> >> I do think your suggested additions would be useful.  In addition, I often
> >> find myself generating a large spreadsheet based on the output of a number
> >> of individual coefficients so that the biologist can use that 
> spreadsheet in
> >> something like Excel to sort and filter data at will.
> >>
> >> While less statistically palatable than the current method and your F-stat
> >> extension, would it be possible to include a third variation such that the
> >> coefficient argument could be set to a vector?  This then leaves the
> >> question of how to "rank" or "sort" genes, but one could choose 
> arbitrarily
> >> to order by the input to topTable (the order of the fit 
> object--I typically
> >> use ALL genes for output) or to use the first value in the coefficient
> >> vector as the "key" coefficient.  For complicated experiments, I 
> think many
> >> biologists like to see how a gene looks for multiple coefficients
> >> simultaneously.
> >>
> >> Thanks,
> >> Sean
> >
> > Hi Sean,
> >
> > I'm not sure what output you are thinking of for vector coef.  How is it
> > different from
> >
> >   write.fit(fit)
> >
> > or
> >
> >   write.fit(fit[,selectedcoefs])
> >
> > ?
>
>It isn't....  Thanks for pointing out the obvious to those of us who didn't
>see it.
>
>Thanks,
>Sean
>
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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