[BioC] Volcano plots

[Gordon Smyth]

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 at 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
>
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