[BioC] Combing Effects (t-stats) from experiment with common reference design?
Ryan C. Thompson
rct at thompsonclan.org
Fri Aug 29 00:09:12 CEST 2014
Typically if you are testing multiple contrasts simultaneously, you
would use an ANOVA test that would five you an F statistics (and
corresponding p-value). But it's not exactly clear if that's what
you're asking for, Can you explain in more detail exactly which
hypothesis you are trying to test? Ar you trying to test whether any of
the Stages is different from the control, or are you trying to test
whether genes are changing between all Stages?
On Thu 28 Aug 2014 12:52:47 PM PDT, Atul wrote:
> Hi All,
> I was wondering whether there is any approach to combine 't-stat' from
> different comparisons but using same control. These are my contrasts:
> Stage1 vs ControlX
> Stage2 vs ControlX
> Stage3 vs. ControlX
> Stage 20 vs. ControlX
> Here the control is same i.e. same sample for all contrasts. From
> 'limma' analysis I have Fold change, t-stats and p-values for each gene.
> Now, is it possible to combine 't-stats' from all different stages to
> single value? Or compute a single combined value for all the contrasts.
> So, that this single metric could be used to rank genes across all time
> points. Is there any package available to do so? I can find methods to
> combine p-values but not the 't-stat'.
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