Dear all, (my sessionInfo() is pasted at the end of this mail for those who are interested) I have a MAList object which contains normalized data of two agilent ChIP on Chip arrays. When I plot the densities with plotDensities() I see one big nice peek at a level of about 9 which I think is the data I want to look at. However, there is also some "noise" at intensities below 5 or even below 0. Is there a way to exclude those spots from my further analysis? If one could plot the densities I guess one should in principle be able to access them in the MAList object but I did not find a way how to do so?! Thanks for any help, Torsten > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] limma_2.18.2 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 AnnotationDbi_1.6.1 DBI_0.2-4 [4] genefilter_1.24.2 grid_2.9.1 lattice_0.17-25 [7] Matrix_0.999375-29 Ringo_1.9.5 RSQLite_0.7-1 [10] splines_2.9.1 survival_2.35-4 tools_2.9.1 [13] xtable_1.5-5 Torsten Waldminghaus Department of Cell Biology Institute for Cancer Research Rikshospitalet-Radiumhospitalet-HF Ullernchaussen 70 0310 Oslo tel: 47-22935973 fax: 47-22934580 e-mail: Torsten.Waldminghaus@rr-research.no http://openwetware.org/wiki/User:Torsten_Waldminghaus [[alternative HTML version deleted]]