[BioC] statistical test for time course data

[Richard Friedman]

Dear Chris,

	The F-test in Limma will tell you if at least one point is different from the others.
It won't tell you which one. 
	The program EDGE (not EdgeR which is a different program entirely) will do
the same based on an model which explicitly takes temporal variation into 
account (this is why I mention it).
	There is also a t-test that deals with whether a single measurement is a member
of the same normal distribution as other measurements. I am not sure off hand, how to
do this in R. If you implement this in R and do it for all the rows, it may be the test that
you want. If you do this, you will be forgoing the empirical Bayesian increase in accuracy 
in Limma or the explicit  temporal modeling in EDGE, but that is up to you. If you do
this, you should current for false discoveries.


With hopes that this help,

Best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave 
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In Memoriam, Hymie Simon
On Jan 31, 2013, at 10:19 PM, chris Jhon wrote:

> Hi Richard,
> 
> Thank you for help.
> In my data ,i have one point which i think it is different from other points and i would like to test statistical significance of the difference of this point.
> Your suggestion means that there is no direct function in R that i can use,i have to use a package which implement an algorithm.
> If so, i think edgeR can do the same analysis too,Am i right?
> 
> Best Reagards,
> Chris
> 
> On Thu, Jan 31, 2013 at 11:53 PM, Richard Friedman <friedman at cancercenter.columbia.edu> wrote:
> Dear Chris,
> 
> 	Limma can be used to test between time points
> treating each time point as a categorical variable.
> The program "EDGE" from the Storey lab, can test whether
> there is significant change over a whole time course.
> 
> http://www.ncbi.nlm.nih.gov/pubmed/16357033
> 
> with hopes that the above helps,
> Rich
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)/
> Columbia Initiative in Systems Biology
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman at cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
> 
> "Complex numbers! Ha! Ha! There is nothing weirder
> than imaginary numbers. Architects don't need to know 
> complex numbers. Whenever I get a  negative root for
> an area, I throw it out. And don't talk to me about
> quaternions. I am not going into computer animation."
> -Rose Friedman, age 16
>  
> 
> On Jan 30, 2013, at 11:43 PM, chris Jhon wrote:
> 
>> Hi All,
>> 
>> I have data at different time points for time course experiment.
>> I have a response for each time point and i would like to test whether the
>> difference between response of two time points is statistically significant
>> or not.
>> my data is linear plot where response on y axis and time on x axis.
>> 
>> what statistical test shall i use?
>> 
>> 
>> I appreciate any help.
>> 
>> Best Regards,
>> Chris
>> 
>> 	
>> [[alternative HTML version deleted]]
>> 
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>