Dear List I have run arrayQualityMetrics with an RG list as input to look at the quality diagnostics for a set of cDNA arrays. There are 28 arrays, but there are only 8 MAplots in the maplot.pdf/maplot.png files. In the other plots I get results for all other arrays (28 boxes in boxplots, 28 subplots in spatial plots and so on). The command to run the arrayQualitMatrics function: aqm.res <- arrayQualityMetrics(expressionset = RG,outdir = "AQM", force=TRUE, intgroup = "Cy3",grouprep = TRUE,do.logtransform = TRUE) I also get a lot of warnings: Warning messages: 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' I hope that someone can give me some hints of why I don't see MAplot for all arrays, and a solution to the warnings > sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=Norwegian (Bokm?l)_Norway.1252;LC_CTYPE=Norwegian (Bokm?l)_Norway.1252;LC_MONETARY=Norwegian (Bokm?l)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokm?l)_Norway.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] arrayQualityMetrics_2.2.2 affyPLM_1.20.0 preprocessCore_1.6.0 gcrma_2.16.0 [5] Biostrings_2.12.8 IRanges_1.2.3 affy_1.22.1 Biobase_2.4.1 [9] plyr_0.1.9 limma_2.18.2 svSocket_0.9-43 svMisc_0.9-48 [13] TinnR_1.0.3 R2HTML_1.59-1 Hmisc_3.6-1 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 AnnotationDbi_1.6.1 beadarray_1.12.0 cluster_1.12.0 [6] DBI_0.2-4 genefilter_1.24.2 grid_2.9.2 hwriter_1.1 KernSmooth_2.23-2 [11] lattice_0.17-25 latticeExtra_0.6-1 marray_1.22.0 RColorBrewer_1.0-2 RSQLite_0.7-2 [16] simpleaffy_2.20.0 splines_2.9.2 stats4_2.9.2 survival_2.35-4 tools_2.9.2 [21] vsn_3.12.0 xtable_1.5-5 > Best regards Ingunn