[BioC] Volcano plots

[James MacDonald]

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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