Hi, I just getting started with bioconductor, so my question might be easy to answer... I have a problem with the read.marrayRaw method. We are not using genepix anymore, we use a new software call BlueFuse . It allow us to save a lot of time as it got a really good method to find the spot and automatically remove the background. It create two new "clean" tif files as well. My problem come after inputting data using marrayLayout , if I take all the data in and then create a marrayRaw I can't find a way to remove afterwards the bad flagged spots or the negative control or the empty spots (which have specific id for the controls or a tag "yes" or "no" for bad flagged (yes means bad flagged). If I removed them before inputting the data I get a error when using read.marrayRaw: Error in "[<-"(`*tmp*`, , f, value = as.matrix(dat[, name.Gf])) : number of items to replace is not a multiple of replacement length I guess it have something to do with the layout and some missing values in block, column... Any idea? Thanks, -------------------------------------------- Julien Bauer, Bioinformatics Research Assistant Micro Array Group Department of Pathology University of Cambridge, Tennis Court Road Cambridge CB2 1QP UK mailto: jb393@cam.ac.uk