[BioC] avereps function

Claus-Jürgen Scholz scholz at klin-biochem.uni-wuerzburg.de
Tue Apr 28 13:19:49 CEST 2009

Dear Erika,

I think avereps simply calculates a mean value - which might be
problematic if your expression values are log transformed after
normalization... Maybe try to apply avereps before normalization and
compare the results to those without averepsing.


Erika Melissari schrieb:
> Dear list,
> does anyone use avereps function by limma package to average probe
> copies on microarray?
> I used this function and obtained a strange result: my differentially
> expressed gene list sensibly change if I use or not this function (I
> perform the average before lmFit and after normalization).
> I know this function only averages probe copies that are on a
> microarray, also if they are in multiple not fixed number.
> What is the problem?
> Thank you very much
> Erika
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