Just to elaborate on Jim's comments, a "volcano plot" is a plot of log-fold-change versus a non-negative statistic which tests the significance of the fold change. Since the size of the statistic tends to increase with absolute log-fold-change, such a plot has the characteristic shape of the open crater of a volcano. Volcano plots are sometimes used to emphasise that variability plays a role in significance as well as fold-change. You don't need any special software to make a volcano plot, you just need the fold change and a suitable test statistic and then do a scatter plot. I don't have my file of papers with me to check, but I seem to remember the term was coined in the paper below. Obviously other authors have used the same idea without necessarily using the name. Cheers Gordon Jin, W., Riley, R. M., Wolfinger, R. D., White, K. P., Passador- Gurgel, G., and Gibson, G. (2001). The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genetics 29, 389 - 395. At 11:33 PM 24/06/2003, James MacDonald wrote: >If you look at pp 14-15 of the limma vignette, you will see a >volcano-like plot and the code to make it. Most of the volcano plots I >have seen plot the log fold change on the x-axis and the -log10(p-value) >on the y-axis. This particular plot uses the log odds for the y-axis, >but the idea is pretty much the same. > >A non-Bioconductor package that explicitly plots a volcano plot is Gary >Churchill's maanova package. You can find the correct website with a >google search for his name. > >HTH, > >Jim > > >James W. MacDonald >UMCCC Microarray Core Facility >1500 E. Medical Center Drive >7410 CCGC >Ann Arbor MI 48109 >734-647-5623 > > >>> <kfbargad@lg.ehu.es> 06/24/03 07:43AM >>> >Dear all, > >recently I was asked about volcano plots. I have the idea that they >are used for detection of differentially expressed genes, but I am not > >quite certain. I think they are a similar representation to scatter >plots. Does anyone know anything about them? any useful links to >explanations? Are volcano plots implemented on any Bioconductor >packages? > >Thanks for your answers > >David > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I too have been wondering about the usefulness of the volcano plot and so was interested in this thread. But (excuse my slowness) what's the answer to the original question about whether they can be used to help detect differentially expressed genes? Matthew > recently I was asked about volcano plots. I have the idea that they > are used for detection of differentially expressed genes, but I am not > > quite certain. -- ---------------------------------------------------------------------- Matthew Hobbs Garvan Institute of Medical Research 384 Victoria St Ph : (02) 9295 8327 Darlinghurst http://www.garvan.org.au email: m.hobbs@garvan.org.au