[BioC] avereps function

[Claus-Jürgen Scholz]

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.

Bests,
Claus-Jürgen

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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