[BioC] statistical test for time course data

[Juliet Hannah]

Hi Gordon,

I've been curious about this as well. Can limma model the following
situation? We have two
treatments and multiple time points. We are interested in if the mean
profile for each treatment
differs over time, treating time continuously. The measurements are
over time for each individual so
we have to account for correlations within individuals. Ideally, I
would like to allow
for a random intercept and a random slope (possible quadratic) if needed.

EDGE uses splines, so that would be nice as well.

I am aware of duplicateCorrelation, Is this the way to proceed?

I'll post a reproducible example for guidance if you indicate that the
above is possible.

Thanks for your time and for your work on limma, which I use frequently.

On Fri, Feb 1, 2013 at 6:46 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> Dear Chris,
>
> Yes, limma can easily test for a difference at one point, or can test for a
> significant change over the whole time course like EDGE.
>
> I don't understand your experiment well enough to give more specific advice.
> You would need to tell us your experimental design, in terms of the targets
> frame, and exactly what you want to test.
>
> Best wishes
> Gordon
>
>> Date: Fri, 1 Feb 2013 12:19:26 +0900
>> From: chris Jhon <cjhon217 at gmail.com>
>> To: Richard Friedman <friedman at cancercenter.columbia.edu>
>> Cc: Bioconductor mailing list <bioconductor at r-project.org>
>> Subject: Re: [BioC] statistical test for time course data
>>
>> 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
>>>
>
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