[BioC] Help for make a dendrogram (philogenetic tree)

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Tue Dec 2 11:09:05 MET 2003

Dear Gordon and All.

Before I having known the Bioconductor, I analyzed some data using software SAM. After I to get the differentially expressed genes, I used program SAMSTER to select these genes. Then, I used the softwares Cluster and the TreeView to group those genes in a dendrogram and a pallete green, neutral and red colors.

I do not know very well what it is in background of this process, but I would like to accomplish the same procedure here. 

Any suggestion is very welcome. Also, I can be wanting to accomplish  something that is not very interesting!

Then, summarizing, I would like to get a dendrogram of differentially expressed genes and one color pallet with green, neutral and red colors indicating the expression (up, neutral or down) of the genes.

I dont now if it is a good idea.

Thanks very much

Best Wishes


On Tue, 2 Dec 2003 14:17:35 +1100 (EST)
"Gordon K Smyth" <smyth at wehi.EDU.AU> wrote:

> 'x' is a symbol which stands for an arbitrary quantity, in this case an
> arbitrary numeric matrix. You are asking, "how can I obtain an arbitrary
> quantity from a limma object", not a meaningful question.
> My guess is that you will want the 'coef' component of your limma
> 'MArrayLM' object, but really you need to decide exactly what it is that
> you want to make a heatmap of, then we can tell you how to obtain it.

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