How would I import a tab delimited file containing geneids and logratios into limma for analysis without going through the low-level reading, normalizing of the cel, gpr, etc. files? Thank you. Karen Vranizan UC Berkeley Functional Genomics Lab

Karen Vranizan wrote: > How would I import a tab delimited file containing geneids and logratios > into limma for analysis without going through the low-level reading, > normalizing of the cel, gpr, etc. files? Thank you. > Karen Vranizan > UC Berkeley Functional Genomics Lab > Limma will take a matrix of values for lmFit. Therefore, all you need to do is to read in your data (using read.table(), for example), remove the columns that do not have gene expression values in them (gene names, ids, etc.) and make a matrix. Then, use the matrix in the call to lmFit like: fit1 <- lmFit(mymatrix,design=design) Where design is your design matrix. Hope that helps. Sean