Hi All, I'm analyzing mouse samples on beadarrays, with the R beadaray package. Using the beadarray help files, I managed to normalize my data, and I know how to annotate them. Now I'd like to clean up the data: - Get rid of multiple entries per genes: my favorite option would be to keep only the median values for genes that are represented by more than 3 probes, and keep only the highest intensity values for genes that are represented by 2 probes. - Get rid of the genes that have a low expression (low intensity) and that have a low variance across the samples (genes that are probably not expressed). My level in R is very limited, I can adapt scripts that I find online to my needs, but I can't really come up with a fresh script from scratch. If you have any links that point out to tutorials that ressemble what I'm trying to do, or other tools that allows to do what I'm trying to do, that would be of great help. Thanks in advance, Sincerely, Laurent (PS: it's my first post here, so please do not hesitate if the content is inappropriate). ### sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C [5] LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.0.6 Biobase_2.10.0 loaded via a namespace (and not attached): [1] limma_3.6.9 [[alternative HTML version deleted]]