model.matrix question
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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia
> 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
Microarray limma Microarray limma • 683 views
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