[BioC] heatmap and cdfenv problems

[lgautier at altern.org]

> 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
>
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>
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