Sorry, this may be a duplicate, but I wasn't subscribed the first time, and I don't know if it went through: Hi all, I was doing an RMA->limma (ebayes) analysis of an affymetrix mouse 430a experiment and noticed that while the p-values listed in toptable were all different, the adjusted p-values (adjust="BH") contained duplicate values. ?I don't think this is incorrect necessarily, but I was wondering why a different alpha wasn't generated for each gene. >From what I understand, the BH method gets the adjusted p-value (alpha) from [P_k*n*c(n) ] / k < alpha, where n = total number of genes (tests), P_k = p-value at kth gene (genes ordered from low to high p-value), and k = number of genes with p-value less than or equal to P_k. ?I'm not entirely sure how the c(n) (dependence correction) part works, but it seems like a unique adjusted p-value (alpha) could be generated for each gene. ?Instead I get: >top<-topTable(efit, adjust="BH", n=nrow(exprs(rmadata))) >write.table(top, "output.xls", sep="\t") from output.xls... ?ID ? ? ? ? ? ? ? ? ? adj.P.Val ? ? ? ? ? P.Value ?Mm.277921 ? ?0.039259664 ? ? 3.17E-06 ?Mm.272646 ? ?0.050424143 ? ? 9.93E-06 ?Mm.148886 ? ?0.050424143 ? ? 1.64E-05 ?Mm.235998 ? ?0.050424143 ? ? 2.02E-05 ?Mm.4598 ? ? ? 0.050424143 ? ? 2.04E-05 ?Mm.10728 ? ? 0.101013086 ? ? 4.89E-05 ?Mm.162744 ? 0.106930684 ? ? 6.34E-05 ?Mm.247564 ? 0.106930684 ? ? 6.91E-05 ?Mm.269384 ? 0.115716969 ? ? 8.62E-05 ?Mm.212428 ? 0.115716969 ? ? 9.34E-05 ?Mm.457989 ? 0.118548889 ? ? 0.000126578 ?Mm.154662 ? 0.118548889 ? ? 0.000128005 ?Mm.21005 ? ? 0.118548889 ? ? 0.000133975 ?Mm.5109 ? ? ? 0.149489879 ? ? 0.000196053 ?Mm.207432 ? 0.149489879 ? ? 0.00020444 Does anyone know why several probesets have the same adjusted p value even though the regular p value is different for each gene? ?I'm 90% sure this is just my ignorance about the BH method, but I'll be very thankful to anyone who can point me in the right direction. ?Thanks in advance, Dave Young > sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base other attached packages: [1] limma_3.8.3 ? ? ? ? ? ? ?mouse430a2mmugcdf_14.1.0 simpleaffy_2.28.0 ? ? ? ?gcrma_2.24.1 [5] genefilter_1.34.0 ? ? ? ?affy_1.30.0 ? ? ? ? ? ? ?Biobase_2.12.2 loaded via a namespace (and not attached): ?[1] affyio_1.20.0 ? ? ? ? annotate_1.30.1 ? ? ? AnnotationDbi_1.14.1 Biostrings_2.20.3 ?[5] DBI_0.2-5 ? ? ? ? ? ? IRanges_1.10.6 ? ? ? ?preprocessCore_1.14.0 RSQLite_0.9-4 ?[9] splines_2.13.1 ? ? ? ?survival_2.36-9 ? ? ? tools_2.13.1 xtable_1.5-6