Dear Thomas, Thank you! It worked! Have a nice weekend! Priscila On Sat, May 9, 2009 at 11:03 AM, Thomas Hampton < Thomas.H.Hampton@dartmouth.edu> wrote: > 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. > > Tom > > > > > 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor >> > > -- 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]]