[BioC] model.matrix question

[Dennis.Burian at faa.gov]

For purposes of creating an experimental design in limma, are model.matrix
and modelMatrix essentially the same or is one preferred over the other?

What is the $qr matrix?

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