[BioC] loop design question

[scholz@Ag.arizona.edu]

Hello,

I'm new to limma and have been plowing through the excellent users guide, where
I've reached a sticking point. Would someone have the saintly patience to
explain to a small mind how the design matrix for the direct design example
works? I think I'm missing something quite fundamental in that I was under the
impression that the numbers 1 and -1 represented the red and green dyes,
respectively, but if that is true, I have no idea what these numbers mean in
columns headed "CD8-CD4" and "DN-CD4". In fact, I don't really understand what
these "subtracted" column headers mean at all, either in the design matrix or
the contrast matrix. I'm planning a loop design experiment and this appears to
be an essential point to grasp. Thanks in advance of your answer.


Matt Scholz
Research Specialist
Department of Plant Science
University of Arizona
scholz at ag.arizona.edu

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