Hi: I have a drug treament experiments with 3 factors (cell lines, compounds, and time course). There are 3 cell lines, 3 compounds (DMSO control, compounds 1 and 2), and 2 time points (4hr and 24hr). When I try to build a design matrix by something like this: design <- model.matrix(~cell.lines*compound*time) I only get 2 cell lines, 2 compounds (DMSO and compound1) and 2 time points. If I use something like this, which is really what I want to compare: design <- model.matrix(~cell.lines + compound + compound*time) I still only get 2 cell lines and 2 compounds in the design matrix. Anything I did wrong? Please help. Thanks, Xia

Xia Han wrote: > Hi: > > I have a drug treament experiments with 3 factors (cell lines, > compounds, and time course). There are 3 cell lines, 3 compounds (DMSO > control, compounds 1 and 2), and 2 time points (4hr and 24hr). When I > try to build a design matrix by something like this: > design <- model.matrix(~cell.lines*compound*time) > I only get 2 cell lines, 2 compounds (DMSO and compound1) and 2 time > points. > If I use something like this, which is really what I want to compare: > design <- model.matrix(~cell.lines + compound + compound*time) > I still only get 2 cell lines and 2 compounds in the design matrix. > > Anything I did wrong? Please help. You didn't do anything wrong, but it appears you don't understand your design matrix. This is a big problem, since it is fundamental to understanding what you are doing. Have you looked at the limma user's guide? There are many examples including time course experiments that are explained in some detail. This is a fairly complex experiment, and you may be better served if you can find a local statistician who can help you analyze these data. Best, Jim > > Thanks, > > Xia > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623