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
.
[[alternative HTML version deleted]]
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
Gordon
> 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
> ...
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
Hi,
thanks a lot for your quick, kind answer and advice.
I will go through it in the coming days.
Michela
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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Il giorno 15/gen/2014, alle ore 00:53, Gordon K Smyth
<smyth@wehi.edu.au<mailto:smyth@wehi.edu.au>> ha scritto:
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
Gordon
Date: Tue, 14 Jan 2014 11:53:11 +0100
From: Riba Michela <riba.michela@hsr.it<mailto:riba.michela@hsr.it>>
To: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>"
<bioconductor@r-project.org<mailto:bioconductor@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
...
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:10}}
