[BioC] LIMMA - generation of design vector for lm using duplicate
wettenhall at wehi.edu.au
Wed Jun 23 14:40:33 CEST 2004
On Wed, 23 Jun 2004, Jakob Hedegaard wrote:
> When ignoring duplicate spots, the functions "readTargets",
> "modelMatrix" and "makeContrasts" helps to construct the
> design matrix.
> Are there similar functions for "automatic" generation of the
> design vector when considering duplicate spots using
> "duplicateCorrelation" and "gls.series"?
In limma, the within-array duplicate spots are handled in a very
different way from the replicate arrays, so while the design matrix
depends on the replicate array structure, it doesn't depend on
the within-array duplicate spot structure, so you can just use
the same functions: readTargets, modelMatrix etc.
Instead of using a design matrix to tell limma about your
duplicate spot structure, you use the ndups and spacing
arguments of the duplicateCorrelation function.
Hope this help,
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