[BioC] Time course experiment....

Sean Davis sdavis2 at mail.nih.gov
Tue Jan 3 13:24:31 CET 2006

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?


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


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