Hi Aedin, I noticed a change in the behavior of your overview function in the made4 package from BioC 2.4 to BioC 2.5. Before, when I only wanted to plot the hc dendrogram, it completely filled the plotting window. However, now no matter what combinations of hc, boxplot and hist, the window is always divided up into 3 sections. I looked at the code, and there seems to be one change that's causing the bug: >overview function (dataset, labels = NULL, title = "", classvec = NULL, hc = TRUE, boxplot = TRUE, hist = TRUE, returnTree = FALSE) { cols = NULL if (sum(boxplot, hist, hc) == 3) layout(matrix(c(1, 1, 2, 3), 2, 2, byrow = TRUE)) if (sum(boxplot, hist, hc) == 2) layout(matrix(c(1, 1, 2, 2), 2, 2, byrow = TRUE)) classvec = as.factor(classvec) This last line is new, and changes the default NULL value into a factor, such that a few lines farther down in the code: if (!is.null(classvec)) { cols = getcol(as.numeric(classvec)) layout(matrix(c(1, 1, 2, 2, 3, 4), 3, 2, byrow = TRUE), heights = c(1.5, 0.1, 2)) } !is.null(classvec) is now TRUE, even if classvec was originally NULL. And since I've e-mailed you, I'll say that I always thought it was weird that the main title for the hierarchical clustering dendrogram was "Histogram", not "Dendrogram": plot(hc, hang = -1, labels = labels, main = paste("Histogram", title, sep = " "), sub = "", xlab = "") Thanks! Jenny > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] limma_3.2.1 affyQCReport_1.24.0 lattice_0.17-26 [4] xtable_1.5-5 simpleaffy_2.22.0 genefilter_1.28.0 [7] made4_1.20.0 scatterplot3d_0.3-29 gplots_2.7.3 [10] caTools_1.10 bitops_1.0-4.1 gdata_2.6.1 [13] gtools_2.6.1 RColorBrewer_1.0-2 ade4_1.4-11 [16] affyPLM_1.22.0 preprocessCore_1.8.0 gcrma_2.18.0 [19] affycoretools_1.18.0 KEGG.db_2.3.5 GO.db_2.3.5 [22] RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.0 [25] affy_1.24.0 Biobase_2.6.0 RWinEdt_1.8-1 loaded via a namespace (and not attached): [1] affyio_1.14.0 annaffy_1.18.0 annotate_1.24.0 biomaRt_2.2.0 [5] Biostrings_2.14.0 Category_2.12.0 GOstats_2.12.0 graph_1.24.0 [9] GSEABase_1.8.0 IRanges_1.4.0 RBGL_1.20.0 RCurl_1.2-1 [13] splines_2.10.0 survival_2.35-7 tools_2.10.0 XML_2.6-0 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu