[BioC] heatmap and cdfenv problems
lgautier at altern.org
lgautier at altern.org
Sat Aug 2 15:00:00 CEST 2008
> Dear BioC list,
> After searching the BioC list and books and googling, I still cannot
> out the questions which are described below. Any suggestions will be
> 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:
> 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
> any alternative way to filter out S. pombe signals??
> By the way, there are lots of cdf files about yeast2, which one is the
> Thank you in advance!!
> R version 2.6.2 (2008-02-08)
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
>  tcltk splines tools stats graphics grDevices utils
>  methods base
> other attached packages:
>  org.Sc.sgd.db_2.0.2 altcdfenvs_1.12.0 makecdfenv_1.16.0
>  yeast2.db_2.0.2 affycoretools_1.10.2 annaffy_1.10.1
>  KEGG_2.0.1 GO_2.0.1 biomaRt_1.12.2
>  RCurl_0.8-1 GOstats_2.4.0 Category_2.4.0
>  RBGL_1.16.0 GO.db_2.0.2 graph_1.18.0
>  siggenes_1.12.0 yeast2_2.0.1 Heatplus_1.8.0
>  RColorBrewer_1.0-2 yeast2cdf_2.0.0 limma_2.12.0
>  geneplotter_1.16.0 lattice_0.17-10 annotate_1.16.1
>  xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-9
>  DBI_0.2-4 multtest_1.18.0 simpleaffy_2.14.05
>  genefilter_1.16.0 survival_2.34-1 affyPLM_1.14.0
>  gcrma_2.10.0 matchprobes_1.10.0 affy_1.16.0
>  preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.3
> loaded via a namespace (and not attached):
>  cluster_1.11.11 grid_2.6.2 KernSmooth_2.22-22 XML_1.93-2.1
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