[BioC] How to carry out time series analysis in Bioconductor

Jenny Drnevich drnevich at illinois.edu
Tue Jul 8 18:59:56 CEST 2008

>the design matrix is such that I compared each total replicate in 
>the treatment i.e A, B, C, and D with E. Thus
>A is compared with E
>B with E
>C with E
>and D with E
>Using BH method in LIMMA analysis how do I carry out a time series 
>analysis of this time course data?
>Any useful suggestions in the area of matrix design and useful codes 
>would be greatly appreciated.

Hi Yemi,

You have a common reference design. Have you read through the limma 
vignette? Try:


See section 7.3 Common Reference Designs on how to create a design 
matrix where each treatment A-D is represented by a column. From 
there, you can go into section 8.8 Time Course Experiments to see how 
to create a contrast matrix to compare specific time points and/or 
use topTableF() to find genes that change over any time point.


>PhD student
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
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e-mail: drnevich at illinois.edu

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