> 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? The man page for heatmap_2 says: " col: the color scheme for 'image'. The default sucks. " Trying may give you a better idea: heatmap_2(x, legend=2) > 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". The details of what you are doing exactly would help the list to help you. Your package versions look a little old (at the scale of R releases). > My abatch at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >