[BioC] how to design matrix by edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Mon May 21 04:37:22 CEST 2012

Dear Shan Gao,

There are many legitimate ways to define a design matrix.  The best way 
depends on what questions you want to answer or what hypotheses you want 
to test.

It looks like you have 35 libraries in total (24 treatment samples and 11 
control samples).  Is this right?  Are all the libraries biologically 

I assume that the control samples have received some sort of inactive 
treatment for the same time period as the active samples.

What is it that you want to test?  Do you want to find DE genes between 
treatment and control at each time?  Or do you want to find genes are DE 
at each time vs 0h, adjusting for control differences?

In any case, you need to create a factors Time and Treatment.  There are 
of length equal to the number of samples (35).  Time takes values from 0 
up to 48.  Treatment takes two values, Treatment or Control, say.

If you can respond to these questions, then I'll give you more help with 
the design matrix and so on.

Best wishes

> Date: Sat, 19 May 2012 19:52:48 -0400
> From: wang peter <wng.peter at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] how to design matrix by edgeR
>        i have a question to ask,  how to design a matrix
> i have such samples
> 0h, 3 replicate and 3 control
> 6h, 4 replicate and 1 control
> 12h, 4 replicate and 1 control
> 18h, 4 replicate and 1 control
> 24h, 3 replicate and 3 control
> 36h, 3 replicate and 1 control
> 48h, 3 replicate and 1 control
> thank you very much
> -- 
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253

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