[BioC] Limma, arrayWeights and fold change

[Amos Kirilovsky]

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
normal?

Regards,

Amos



Dr. Amos Kirilovsky
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