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

[Sean Davis]

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