[BioC] Limma/Time Course Experiments

Mark Robinson mrobinson at wehi.EDU.AU
Wed Sep 19 23:40:41 CEST 2007


Hi Lana.

Try:

topTable(fit2,coef=1:2)

This will sort on an F statistic for that set of contrasts/coefficients.

Cheers,
Mark


On 20/09/2007, at 5:39 AM, Lana Schaffer wrote:

>
> Hi,
> In the User's guide the list of genes which
> correspond at either the 6 or 24 hour times
> is accessed by
>> selected.wt <- p.adjust(fit2$F.p.value, method="BH") < 0.05
> However I want the table from topTable.  So now I am using both
>> topTable(fit2, coef=1)
>> topTable(fit2, coef=2)
> to get the statistics and then using the list from the selected
> command.
> How do you suggest that I get the topTable but using both
> contrasts in one statement?
>
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
>
>
>
>
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