[BioC] limma for time course dataset 2

[Yunshun Chen]

Hi Joseph,

The way to analyse a time-course experiment depends on what scientific
question you want to answer.
If, say, you are interested in the difference between time 1 and time 2 for
all 21 subjects, then you can compare those two groups using the standard
one-way layout analysis.
If you are interested in whether the expression levels of the genes change
along the time, then you can analyse the data by fitting a trend using a
regression spline or a polynomial.

There is no information on how you fit your data and what you are trying to
find. 
Did you use the one-way layout approach or fit a regression spline trend? 
That determines the meaning of the coefficients in your output.
In other words, what 'coef' to use for the 'topTable' depends on what model
you fit to your data and what question you want to answer.

There is a time course experiment case study in the limma user's guide
(section 9.6).
It might be helpful to answer your question.

Regards,
Yunshun

-----------------------------
Yunshun Chen,
Research Officer,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research, 
1G Royal Parade, Parkville, Vic 3052, Australia.
Email: yuchen at wehi.edu.au



------------------------------

Message: 14
Date: Tue, 18 Feb 2014 15:15:21 +0800
From: Joseph J Hou <houjue00722 at sina.com>
To: smyth <smyth at wehi.EDU.AU>
Cc: bioconductor <bioconductor at stat.math.ethz.ch>
Subject: [BioC] limma for time course dataset 2
Message-ID: <2014021815152088222923 at sina.com>
Content-Type: text/plain


Hi Gordon,
If I have multiplex time points, when set coeff to "NULL" in topTable
function, it return results (named as R1) from F-statistics, however, if I
set coeff to each time point, one by one, then I get DEG in each time point
(named as R2, combined all DEG symbol in one list). Then, R1 and R2 have
some overlap, but R2 usually has more genes that excluded in R1. ?So, in
this case, which approach back correct DEG gene list? ?

Best,
Joe



Joseph J Hou
----------------------------------------------

Jue Hou Ph.D.
Research Assistant

Center of Medical Physics and Technology
Hefei Institutes of Physical Science
Chinese Academy of Sciences
No.350 Shushanhu Road,Shushan District,Heifei,P.R. China
Tel. +86551-65595385
Email: joseph.houjue at gmail.com; houjue at cmpt.ac.cn
?7"<~HK#:?Joseph J
Hou7"KMJ1<d#:?2014-02-17?10:30JU<~HK#:?smyth3-KM#:?bioconductorVwLb#:?limma
for time course dataset
Hi?Gordon,
My project is time course dataset, 9 time points and 21 subjects. When I use
"topTable" function to call differential genes, how to set argument "coeff"
? If I set it as each time point (column name specifying) one by one, it'll
reture results by t-test. ??If I set to as "NULL", topTable will use
F-ststistic to rank genes with all coefficient, and usually the difference
gene by F- test will smaller than t-test by each time points. I'm worry
about F-ststistic will miss some of meaning informations. So, as you
suggestion, how to set the coeff parameter to time-course dataset, to find
allover DEG and DEG in individual time point??p.s. Usually, in heatmap
figure, log-Fold change or normalized intensity of each group used in
visualization??

Best,Joe



Joseph J Hou
----------------------------------------------

Jue Hou Ph.D.
Research Assistant

Center of Medical Physics and Technology
Hefei Institutes of Physical Science
Chinese Academy of Sciences
No.350 Shushanhu Road,Shushan District,Heifei,P.R. China
Tel. +86551-65595385
Email: joseph.houjue at gmail.com; houjue at cmpt.ac.cn


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