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

Gordon K Smyth smyth at wehi.EDU.AU
Tue Jan 3 13:40:57 CET 2006

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





In general, the use of contrasts is intended for looking at subsets of coefficients.  E.g.,
contrasts.fit() followed by topTable() with coef=NULL could rank genes on the F-statistic for any
selection of coefficients or contrasts.

My thought of what a vector coef argument to topTable() would be is that it should (i) compute the
fit object for the set of contrasts defined by those coefficients and (ii) output a top-table
ranked by the F-statistics for that set of contrasts.


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