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

Marcelo Luiz de Laia mlaia at fcav.unesp.br
Mon Dec 1 14:43:32 MET 2003

Hi All,

I read the help about mva heatmap and I see that it have the argument 'x' (numeric matrix of the values to be plotted).

In my case, I normalized my data with marrayNorm and calculated the differentially expressed genes with limma.

In limma I have MA, but I do not know how do I do to extract the 'x' values (top 50 diferentially genes).

'x' is the MA value in limma?

I look in limma help but I did not obtain success.

Would can you suggest me a other document especific about how do I do or a step that explains how do I do to obtain 'x' from the limma object?



On Sun, 30 Nov 2003 19:17:09 -0200
Marcelo Luiz de Laia <mlaia at fcav.unesp.br> wrote:

> Dear All,
> I analyse my datas using marray and limma packages, with yours helps, sure! Thanks very much!
> Now, I have the differentially expressed genes and I would want to have a dendrogram of these genes.
> Like this:
>    |--------Gene1
> ---|
>    |     |--Gene2
>    |-----|
>          |--Gene10
> Is it possible make this?
> What packages I use for this?
> All tips and helps are welcome.
> Thanks very much
> Marcelo
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