[BioC] limma and nested factors

Arne.Muller at aventis.com Arne.Muller at aventis.com
Thu Apr 8 16:47:00 CEST 2004


thanks for reply. I guess you mean is to use the rank as given by topTable
(by p-value) for one contrast for a comparison with another contrast? Since
the rank is already given (by topTable) would I've to use a pearson

What I've just tried is a simple pearson (the data look not too far from
normal) and spearman correlation separate for up and downregulated genes.

> cor.time.spearman
               down          up
NEWvsOLD  0.4461673 0.371619276
NEWvsPRG -0.1675682 0.003799389
OLDvsPRG -0.1500851 0.057734972

> cor.time.pearson
                 down         up
NEWvsOLD  0.723402369 0.49514365
NEWvsPRG -0.035844726 0.01057829
OLDvsPRG  0.005358755 0.04535618

Given are the "estimates". The correlation is based on the coefficients in
the eBayes fit from limma. Only those coefficients were included for which
either one or the other (e.g. NEW or OLD) provides a coefficient >0 (up) with
p<=0.01, or <0 for down. For each correlation between 500 and 1000 genes are

This is not too far from what I expect, since OLD and NEW have been generated
using quite similar experimental protocols. It also tells that these batches
don't have that much in common ...

	thanks for your suggestion,


Arne Muller, Ph.D.
Toxicogenomics, Aventis Pharma
arne dot muller domain=aventis com

> -----Original Message-----
> From: Stephen Henderson [mailto:s.henderson at ucl.ac.uk]
> Sent: 08 April 2004 15:06
> To: 'Gordon Smyth '; Muller, Arne PH/FR
> Cc: 'bioconductor at stat.math.ethz.ch '
> Subject: RE: [BioC] limma and nested factors
> how about the rank spearman correlation of all the toptable p-values?
> >There seems nothing wrong with your limma analysis. Focusing 
> only on the
> >most extreme differentially expressed genes as you do with a 
> toptable will 
> >of course exaggerate the differences between the three labs.
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