[Bioc-devel] Making hypothesis testing easier with design matrices?
Ryan C. Thompson
rct at thompsonclan.org
Tue Dec 11 10:59:54 CET 2012
On 12/10/2012 11:06 PM, Gordon K Smyth wrote:
> I don't see a proposal below, only a question.
Yes, I ended up not really proposing anything because I realized that I
didn't really have anything that improves on linear modeling. But see
below for what I was trying to get at.
> What linear modelling programs such as limma and edgeR do is not
> "simply computing logCPM individually for each sample and taking the
> mean of all the samples in each group".
This what I thought, and I just wanted to make sure. Which brings me to...
> I think that it might be better for you to try to understand what
> linear modelling is doing in a more sophisticated and complete manner
> before trying to redesign the process. What about reading a textbook
> on linear modelling?
This is exactly what I will do.
However, I want to clarify that I'm not trying to redesign the process
of linear modeling. I'm trying to find a middle ground between simple
but inflexible two-group comparisons and flexible but confusing (for
biologists that I work with, and sometimes for me) linear modeling in
its full generality. I think my idea of a no-intercept factor of
interest plus sum-to-zero blocking factors accomplishes that goal for my
purposes. It is a subset of the full possibilities of (generalized)
linear modelling, but one which (unlike simple two-group comparisons)
encompasses every experimental design I've encountered with so far, and
does so in a way that makes sense to my biologist collaborators, since
each group mean gets its own coefficient in the design matrix.
Thank you, Gordon, for your patience with me as I stumble around with my
limited understanding of linear modelling. I will try to find a good
textbook on the subject and improve my understanding.
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