[BioC] avereps function

Erika Melissari erika.melissari at bioclinica.unipi.it
Tue Apr 28 14:39:46 CEST 2009

Dear Claus-Jürgen,

on avereps help I read:

A new data object is computed in which each probe is represented by the 
average of its replicate spots. For an MAList object, the components M and A 
are both averaged in this way, as weights and any matrices found in 
For an MAList object, ID defaults to MA$genes$ID is that exists, otherwise 
to rownames(MA$M).

If x is of mode "character", then the replicate values are assumed to be 
equal and the first is taken as the average.

Avereps schould works on an MA object, that is after normalization. If his 
object is not an MA list, it works like uniquegenelist function I think, and 
does not perform the average.


----- Original Message ----- 
From: "Claus-Jürgen Scholz" <scholz at klin-biochem.uni-wuerzburg.de>
To: <erika.melissari at bioclinica.unipi.it>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, April 28, 2009 13:19 PM
Subject: Re: [BioC] avereps function

> 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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