[BioC] DESeq /edgeR design problem for a small RNASeq
Simon Anders
anders at embl.de
Tue Jun 4 11:52:58 CEST 2013
Hi Eduardo
Thanks for the exaplanation. I now see what yiu are heading at.
On 04/06/13 11:01, Eduardo Andrés León wrote:
> (MTsD - MTcD) - (WTsD -WTcD) = Real effect of the overexpression.
Yes, this is precisely what is called an "interaction effect" and
described in R's formula notation with ":" operator.
So, you use, as full model:
full_model <- fitNbinomGLMs( cds, count ~ mutation + drug + mutation:drug)
and as reduced model
reduced_model <- fitNbinomGLMs( cds, count ~ mutation + drug )
and then compare the two:
pvals <- nbinomGLMTest( full_model, reduced_model )
(As an alternative for the notation "~ A + B + A:B", you will often see
the equivalent abbreviated notation "~ A * B".)
If you deal with such questions more often, it may be helpful to read a
textbook on linear models and Anova. This is all quite standard stuff.
Simon
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