[BioC] Stange tailing in a Volcano-plot
valtteri at biotech.kth.se
Thu Nov 6 09:54:26 MET 2003
I have a question regarding the Volcano-plots which can be obtained after
an analysis using the linear models in the limma package.
In some cases I see a strange tailing phenomena in the Volcano-plot (x=M
and y=eb$lods). I think this is a mathematical "artefact" and would
appreciate if someone could explain this to me.
This tailing looks like an inversed "normal distribution plot", and where I
by inversed mean an up-side-down distribution plot with the lowest eb$lods
values at M=0.
The image is available as a pdf file at
What I noticed is that the features in this tail have their s2.post values
equal to 0.0663 in the object obtained using the ebayes function of the
limma package. In the image provided I have coloured all features with
s2.post=0.0663 in red.
Some background on the analysis I did:
R version: 1.8.0
Limma version: 1.2.8
The data is background subtracted, filtered and normalised data from 5
slides with 30 000 features (no duplicates), stored in a numeric matrix, Ms
fit <- lm.series(Ms, design=c(1,1,1,1,1))
eb <- ebayes(fit)
M <- fit$coef # to get the M values
plot(M, eb$lods) # to give the volcano-plot
I'd really appreciate if someone could explain strange (?) behaviour to me.
Department of Biotechnology, KTH
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Email: valtteri at biotech.kth.se
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