[BioC] Limma, arrayWeights and fold change

Amos Kirilovsky amos.kirilovsky at gmail.com
Thu Aug 2 17:01:15 CEST 2012

Dear list,

I'm using the limma package and the arrayWeights function to make some
transcriptomic analysis: One group of samples versus an another group.
arrayWeights allow me to get very interesting results but in
documentation it says you need replicates. Are they technical or/ and
biological replicates? I couldn't find clearly the information.

My second question is: can arrayWeights introduce some bias? for
example in one of my analysis with 2 groups and 5 samples by group,
the weights found by arrayWeights are:
for the 1st group : 2.91 0.99 0.43 2.18 0.89
for the 2nd group : 1.40 1.24 0.29 1 .40 0.60
It seems that the weights are in general higher for the first group.
Is that a problem?

Next in limma, when Weights calculated by arrayWeights are implemented
to the the lmFit function how are calculated the log2 fold change
(coefficients ) ?
I tried to calculate them by myself applying the weights to the
samples but I couldn't get the same results.
I observed that the average expression of each probe with or without
applying the weights is equal with the function topTable. Is that



Dr. Amos Kirilovsky
Institut fédératif  de Recherches (IFR) 113 : Immunité-Cancer-Infection
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