[BioC] Stange tailing in a Volcano-plot

Valtteri Wirta valtteri at biotech.kth.se
Thu Nov 6 09:54:26 MET 2003

Dear Group,

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.


best regards,

Contact information:

Valtteri Wirta
Department of Biotechnology, KTH
AlbaNova University Center
S - 10691 Stockholm, Sweden

Visiting address: Roslagstullsbacken 21, B3
Phone: +46 8 5537 8344(office)
Phone: +46 733 386 341 (gsm)
Fax: +46 8 5537 8481
Email: valtteri at biotech.kth.se
Web: www.biotech.kth.se/molbio

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