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

[Gordon K Smyth]

> 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?

'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.

Gordon

> Thanks
>
> Marcelo
>
> 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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