[BioC] model.matrix question

[Gordon K Smyth]

> Date: Thu, 5 Jun 2008 14:31:11 -0500
> From: Dennis.Burian at faa.gov
> Subject: [BioC] model.matrix question
> To: bioconductor at stat.math.ethz.ch
>
> For purposes of creating an experimental design in limma, are model.matrix
> and modelMatrix essentially the same or is one preferred over the other?

modelMatrix() is only for two colour arrays. model.matrix() is only for 
single channel arrays (or possibly two-colour arrays with a common 
reference always on the same channel).

The limma help page help("06.LinearModels") says:

"Design matrices for Affymetrix or single-color arrays can be created 
using the function model.matrix which is part of the R base package. The 
function modelMatrix is provided to assist with creation of an appropriate 
design matrix for two-color microarray experiments."

> What is the $qr matrix?

help("qr")

If the qr help page doesn't make sense to you, as it probably won't if 
you're not into numerical linear algebra, then you probably don't need to 
know.

Best wishes
Gordon

> Thanks,
>
> Dennis Burian, Ph.D.
> Functional Genomics Group
> Civil Aerospace Medical Institute, AAM-610
> 6500 S. MacArthur Blvd.
> Oklahoma City OK  73169
> 405-954-6087
> dennis.burian at faa.gov