Hello everyone, I would like to perfom a linear model like the following on my data using limma but i am not familiar with that. Y~ a + b*TYPE + c*TIME + d * TYPE * TIME I have 2 types of mice, CSB and WT, and 3 time points. I would like to model the time as a continous covariate. Unfortunately, the limma examples i found contain only categrical covariates. Can anybody provide me any help? Or does anybody know where to find an example of limma model with continous covariate. Dimitris Kampas [[alternative HTML version deleted]]

Hi Dimitris, On 6/30/2011 3:24 PM, Dimitris Kampas wrote: > Hello everyone, > > I would like to perfom a linear model like the following on my data using > limma but i am not familiar with that. > > Y~ a + b*TYPE + c*TIME + d * TYPE * TIME > I have 2 types of mice, CSB and WT, and 3 time points. > I would like to model the time as a continous covariate. > Unfortunately, the limma examples i found contain only categrical > covariates. > Can anybody provide me any help? Or does anybody know where to find an > example of limma model with > continous covariate. You don't say what kind of data you are analyzing, so I will keep this pretty general. What you need to understand is that the design matrix set up by R is dependent on the class of the input data. So if you pass numerical data to model.matrix(), then R will assume you want to model those data as a continuous variable. For example, > z <- 1:4 Fit z as a continuous variable: > model.matrix(~z) (Intercept) z 1 1 1 2 1 2 3 1 3 4 1 4 attr(,"assign") [1] 0 1 Fit z as factor levels: > model.matrix(~factor(z)) (Intercept) factor(z)2 factor(z)3 factor(z)4 1 1 0 0 0 2 1 1 0 0 3 1 0 1 0 4 1 0 0 1 attr(,"assign") [1] 0 1 1 1 attr(,"contrasts") attr(,"contrasts")$`factor(z)` [1] "contr.treatment" Does that help? Best, Jim > > Dimitris Kampas > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues