Hi, Gordon,
thanks for reply


I'm sorry for giving the impression of naiveness,
anyhow,
I have forwarded the previous email to which you have answered because it contained the same design
explicitly defined, the design is derived from the limma vignette

X <- ns(limmaTargets$Time,df=4)
design<-model.matrix(~Group*X) #here Group refers to the different 6 experimental groups)

My point regards the possibility and way to extract genes which differ in the different experimental groups (that unfortunately yesterday I mentioned as treatments)
not compared with the control, or better which could be the best way to solve this, for example reasoning simply on venn diagram of the single results
as was for example done using the maSigPro package for time series analysis in gene expression.

The point regards exactly  which could be the most convenient way to design the analysis
-compare just 2 time series (control and experimental group1) just with control and one experimental group
-make a design matrix to compare different experimental groups with control o among each other

in the trail I performed with the contrast matrix option as referred below (goup1 is the experimental group 1 and group2 the experimental group 2)
I have obtained discouraging results as mentioned

I've tried to write something like:

contrast.matrix <- makeContrast("(sum of the X.coefficient for group 1) - (sum of the X.coefficient for group2)", levels=design)

In my first attempt I've set group2 the same as control, this to see if
the explicit contrast gives the same results as the standard analysis.
Alas, it doesn't.

Hoping this sounds clear
I attach the simplified design


hoping to receive your important and kind feedback

Michela

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)

Il giorno 11/mar/2014, alle ore 23:20, Gordon K Smyth <smyth@wehi.EDU.AU<mailto:smyth@wehi.EDU.AU>> ha scritto:

ExpG1, ExpG2 are experimental groups

Dr. Michela Riba
Genome Function Unit
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

lab: +39 02 2643 9114
skype: mic_mir32
riba.michela@gmail.com<mailto:riba.michela@gmail.com>
riba.michela@hsr.it


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