heatmap and cdfenv problems
0
0
Entering edit mode
@lgautieralternorg-747
Last seen 6.6 years ago
> 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 >
Annotation GO yeast2 cdf Heatplus Annotation GO yeast2 cdf Heatplus • 475 views
ADD COMMENT

Login before adding your answer.

Traffic: 459 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6