[BioC] LIMMA - generation of design vector for lm using duplicate spots?

[James Wettenhall]

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"?

Jakob,

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,
James