[BioC] About Volcano Plot
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?
> 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
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