Hi all, I am doing some analyses of Affy arrays using limma. Following the manual, I generated the fit2 object using the default eBayes settings, and topTable with (almost) default settings. > dim(eset) Features Samples 22625 15 > fit <- lmFit(eset,designMATRIX) > fit2 <- eBayes(contrasts.fit(fit,contrast.matrix)) > TT <- topTable(fit2,adjust.method="BH",number=length(fit2$genes)) I am now using decideTests, and have read the help that goes with it. However, I still can't decide (no pun intended) on what is the best method ("separate", "global", "hierarchical", "nestedF") to apply with what adjust.method ("none", "BH", "fdr", "BY", "holm"). I have so far left adjust.method as "BH", and varied the method. I can chose one (global) that gives me most of the genes I "want", but I'd rather chose the method more objectively. I have 5 contrasts, so am guessing from the email archives that nestedF is probably not appropriate for so few contrasts? Are there any general guidelines as to which is the best method to use when? Thanks in anticipation, a > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] statmod_1.3.1 celeganscdf_2.0.0 arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 [6] simpleaffy_2.14.05 affyPLM_1.14.0 gcrma_2.10.0 matchprobes_1.10.0 RColorBrewer_1.0-2 [11] vsn_3.2.1 genefilter_1.16.0 survival_2.34 geneplotter_1.16.0 lattice_0.17-2 [16] annotate_1.16.1 xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4 [21] celegans_2.0.1 affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 [26] limma_2.12.0 loaded via a namespace (and not attached): [1] KernSmooth_2.22-21 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.