Dear BioC list, After searching the BioC list and books and googling, I still cannot figure out the questions which are described below. Any suggestions will be really appreciated. 1. I have wt, mut-a, mut-b strains, each of them has 2 replicates. After implementation of heatmap_2 function in Heatplus package, I got result and understand how the dendrogram is generated, but I am confused that how to interpret the color assigned to each of the genes. Supposed gene-x is red( fold-change : -2), what it is relative to? to wt or to overall samples? 2. I tried to use altcdfenv package to only get the S. cerevisiae environment, however, I always got error in the first step to wrap the environment: "Error in validObject(.Object) : invalid class "CdfEnvAffy" object: invalid object for slot "envir" in class "CdfEnvAffy": got class "CdfEnvAffy", should be or extend class "environment". My abatch@cdfName is "Yeast_2" and annotation file is yeast2. Or if there is any alternative way to filter out S. pombe signals?? By the way, there are lots of cdf files about yeast2, which one is the most updated? Thank you in advance!! Hui-Yi R version 2.6.2 (2008-02-08) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk splines tools stats graphics grDevices utils datasets [9] methods base other attached packages: [1] org.Sc.sgd.db_2.0.2 altcdfenvs_1.12.0 makecdfenv_1.16.0 [4] yeast2.db_2.0.2 affycoretools_1.10.2 annaffy_1.10.1 [7] KEGG_2.0.1 GO_2.0.1 biomaRt_1.12.2 [10] RCurl_0.8-1 GOstats_2.4.0 Category_2.4.0 [13] RBGL_1.16.0 GO.db_2.0.2 graph_1.18.0 [16] siggenes_1.12.0 yeast2_2.0.1 Heatplus_1.8.0 [19] RColorBrewer_1.0-2 yeast2cdf_2.0.0 limma_2.12.0 [22] geneplotter_1.16.0 lattice_0.17-10 annotate_1.16.1 [25] xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-9 [28] DBI_0.2-4 multtest_1.18.0 simpleaffy_2.14.05 [31] genefilter_1.16.0 survival_2.34-1 affyPLM_1.14.0 [34] gcrma_2.10.0 matchprobes_1.10.0 affy_1.16.0 [37] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.3 loaded via a namespace (and not attached): [1] cluster_1.11.11 grid_2.6.2 KernSmooth_2.22-22 XML_1.93-2.1 [[alternative HTML version deleted]]