[BioC] multiple groups time course RNA Seq LIMMA

Gordon K Smyth smyth at wehi.EDU.AU
Wed Jan 15 00:53:42 CET 2014

Dear Riba,

The advice given in Section 9.6.2 of the User's Guide will still work fine 
even when Group as more than two levels.

Just type colnames(fit) and it will be obvious which coefficients 
correspond to which experimental group.

Yes, you could use contrast.fit() if you wish, but there seems to me to be 
no reason to do so.

Best wishes

> Date: Tue, 14 Jan 2014 11:53:11 +0100
> From: Riba Michela <riba.michela at hsr.it>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] multiple groups time course RNA Seq LIMMA
> Hi,

> I'm approaching a RNA-seq experiment concerning the analysis of a time 
> course of 5 time points in 6 experimental groups (including Control 
> group).

> As an example:
> FileName Group Time
> a Control 6hr
> b Control 24h
> ...
> e ExpG1 6hr
> f ExpG1 24hr
> ...
> l ExpG2 6hr
> m ExpG2 24hr
> ...
> (ExpG1, ExpG2 are experimental groups)
> I'm going to use LIMMA for extraction of time changing genes in the 
> single experimental groups compared to Control group.
> I'd like to see how to extract this result in the topTable (i.e. which 
> coefficients select) for each single comparison of the experimental 
> group towards Control) since from the provided example in the LIMMA 
> manual (pag. 49) such topTable is referred to a design concerning one 
> single experimental group towards Control in a time course instead of 
> multiple experimental groups.
> Is there in addition the possibility to design a contrast matrix in such 
> situations or is it better to consider topTables using various 
> coefficients blocks?
> Thanks a lot for your answer
> Michela Riba
> ...
> Dr. Michela Riba
> Genome Function Unit
> Center for Translational Genomics and Bioinformatics
> San Raffaele Hospital
> Milano
> ...

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