[BioC] [Bioc-devel] Draw volcanoplot in Limma

[Gordon K Smyth]

[Moved from Bioc-devel]

> Date: Mon,  7 Nov 2005 09:32:39 -0600
> From: Edoardo Giacopuzzi <gedoardo at bluebottle.com>
> Subject: [Bioc-devel] Draw volcanoplot in Limma
> To: bioc-devel at stat.math.ethz.ch
>
> Hi, I'm using from little time to analyze my microarray data.
> After using eBayes() function to compute the odds ratio for my genes
> now i want to draw a volcano plot showing my data.
> I've used the volcanoplot() function as follow:
>
>> volcanoplot(fitNorm, highlight=500, names=fitNorm$genes$ID)
>
> and I get a volcano plot with 500 gene highlighted, each one with his
> name... So the resulting graph is quite confused!
>
> I want to know if there is a way to obtain a volcano plot with dots
> rapresenting my top-500 genes designed, for example, in a different
> color (but without names labels).
>
> Thanks!
> Edo

Dear Edo,

No there's no way to highlight points in a volcanoplot without labels, although there probably
should be because, as you say, a large number of labels is quite confusing.

Note that I've moved this thread to the bioconductor mailing list.  (You've sent three limma
questions now to three different lists.  Seriously, only the Bioconductor list is appropriate for
queries about using Bioconductor packages.)

Best wishes
Gordon