Re: [R] limma contrast matrix

2011-08-04 Thread Patrick Breheny
On 08/04/2011 08:53 AM, Belmont, John W wrote: I am trying to correct for the effect of 2 covariates in a gene expression data set. design<-model.matrix(~0 + Factor + cov1 + cov2) QUESTION: How to set up the contrast matrix? The usual commands fit <- lmFit(selDataMatrix, design) cont.matrix

Re: [R] limma contrast matrix

2011-08-04 Thread James W. MacDonald
Hi John, The limma package is part of Bioconductor, so you should be asking this question on the BioC listserv rather than R-help. In addition, please see the posting guide. The example you give is not self-contained, and the term 'does not work' is so unspecific as to be useless. On 8/4

[R] limma contrast matrix

2011-08-04 Thread Belmont, John W
I am trying to correct for the effect of 2 covariates in a gene expression data set. design<-model.matrix(~0 + Factor + cov1 + cov2) QUESTION: How to set up the contrast matrix? The usual commands fit <- lmFit(selDataMatrix, design) cont.matrix <- makeContrasts(FacCont=Group1-Group2, level