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Old 06-27-2013, 04:08 AM   #3
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Join Date: Apr 2011
Posts: 60

Originally Posted by dpryan View Post
You'll want option (2). This happened to be recently discussed on the bioconductor email list, so have a look at that thread.
Hi @dpryan:

That's a really relevant post, and it's convenient to include the subject effect in the GLM setting ;-)

Can I know if, according to my design matrix above, the following formula are correct?

f_dispersion = count ~ sample + (condition + subject) * exon
Null model: f_0 = count ~ sample + subject * exon + condition
Alternative model: f_1 = count ~ sample + subject * exon + condition * I(exon == exonID)

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