Dear All, I have been using the Limma library in the R package. I need to write an output of an analysis into a file of a text or .csv format. I tried using the "save" and "dump" functions in R to accomplish the same but without any success. All I get is a 1kb file with a link to the results file. How can I save the results(380000 spots) of an analysis into a test file outside R? In the arrays I am using, the number of replicate spots for each probe is not constant. So what value do I use for ndups in fit <- lmFit(MA,design,ndups=?,correlation=0.579) Is there a method in Limma which takes care of such discrepancies in the number of replicate spots for each probe? If not, is there an assumption I can make for the same? -Ankit