[BioC] loop design question

[Gordon K Smyth]

> Date: Wed, 3 Aug 2005 08:27:13 US/Arizona
> From: scholz at Ag.arizona.edu
> Subject: [BioC] loop design question
> To: bioconductor at stat.math.ethz.ch
>
> 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.

The headers mean that the coefficients represent the comparisons CD8 vs CD4 and DN vs CD4
respectively.  As the text explains, the other two treatments are compared back to CD4.

The easiest way to analysis a direct design is to choose one of the treatments to compare back to
in this way, i.e., to stand in as a virtual common reference.  The design matrix for the CD
example could have been computed using

design < modelMatrix(targets, ref="CD4")

Just use the modelMatrix() function, look at the 1's and -1's, just understand what the
interpretatation of the columns is in terms of treatment comparisons.

Gordon

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