Dear all, I have been using normalize.loess and I get the following error message when my matrix contains NA values: > my.mat = matrix(nrow=100, ncol=4, runif(400) ) > my.mat[1,1]=NA > my.mat.n = normalize.loess(my.mat, verbose=TRUE) Done with 1 vs 2 in iteration 1 Done with 1 vs 3 in iteration 1 Done with 1 vs 4 in iteration 1 Done with 2 vs 3 in iteration 1 Done with 2 vs 4 in iteration 1 Done with 3 vs 4 in iteration 1 1 0.317319 Warning messages: 1: In means[, j] + aux : ?longer object length is not a multiple of shorter object length 2: In means[, k] - aux : ?longer object length is not a multiple of shorter object length ... Is that normal? I'm scared that this introduces abnormalities in the normalization. Thanks for your help, Emmanuel > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-pc-linux-gnu locale: LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines ? tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets [8] methods ? base other attached packages: ?[1] limma_2.16.3 ? ? ? ?GOstats_2.4.0 ? ? ? Category_2.4.0 ?[4] genefilter_1.22.0 ? survival_2.34-1 ? ? RBGL_1.16.0 ?[7] annotate_1.20.1 ? ? xtable_1.5-4 ? ? ? ?GO.db_2.2.0 [10] AnnotationDbi_1.2.2 RSQLite_0.6-9 ? ? ? DBI_0.2-4 [13] graph_1.18.0 ? ? ? ?YEAST_2.0.1 ? ? ? ? affy_1.20.0 [16] Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 ? ? ? ?cluster_1.11.11 ? ? ?preprocessCore_1.4.0 [4] tcltk_2.8.0