
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
Е.
e ExpG1 6hr
f ExpG1 24hr
Е
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


ЕЕ.

Dr. Michela Riba
Genome Function Unit
Center for Translational Genomics and Bioinformatics
San Raffaele Hospital
Milano
ЕЕЕ.



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