[BioC] avereps function

[Claus-Jürgen Scholz]

Dear Erika,

I've read that too and of course avereps accepts MAList objects, so from
that point of view the application of avereps is absolutely correct.
However, as far as I remember (I hardly work with limma), the M and A
values are somehow log-transformed, and avereps simply calculates an
average (at least in an initial check that has not been performed on an
MAList). Imagine intensities from replicated spots (for simplicity in
log10), say 2 and 4. Obviously the average of these values is 3, but
re-converted to linearity, the values 100 and 10000 are NOT averaged to
1000. Maybe that's the point...

Bests,
Claus-Jürgen


Erika Melissari schrieb:
> 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 object$other.
> For an MAList object, ID defaults to MA$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.
>
> Erika
>
>
> ----- 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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