[BioC] About Volcano Plot

Thomas Hampton Thomas.H.Hampton at Dartmouth.edu
Sat May 9 16:03:28 CEST 2009

It isn't too hard to make your own volcano, and I do it
all the time. You may find it easier to just use the R
plot command like this rather than trying to wangle something in
your bioconductor package:

plot(M, -log10(P), pch = '.')

assuming M is your vector of log2 fold differences and P
is a vector of whatever you prefer as a significance measure.

A very nice thing about doing it yourself is that you can then
highlight a set of genes that interest you:

points(M[interesting], -log10(P[interesting]), col = "red", pch = 16)

Of course you can add all sorts of labels in the plot command.


On May 9, 2009, at 9:47 AM, Priscila Grynberg wrote:

> Dear BioCs,
> I'd like to make a volcano plot, but instead of B value, I want to  
> plot the
> adjusted p-values. Can I do that? Fold-changes X adjusted p-values?
> I have oligo slides. Do you need any further information for that?
> Thanks,
> Priscila
> -- 
> Priscila Grynberg, B.Sc., M.Sc.
> Doutoranda em Bioinformática (Bioinformatics D.Sc student)
> Laboratório de Genética Bioquímica
> Universidade Federal de Minas Gerais
> Tel: +55 31 3409-2628
> CV: http://lattes.cnpq.br/8808643075395963
> 	[[alternative HTML version deleted]]
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