[BioC] Average expression value from limma

[Gordon K Smyth]

Dear Ekta,

The AveExpr in the topTable from limma is the ordinary arithmetic average 
of the log2-expression values for the probe, across all arrays in the 
experiment.  This is exactly as described in the documentation.

There is no quantity called "Ave.Expr.from.limma" in any limma output.

Best wishes
Gordon

> Date: Mon, 20 May 2013 16:45:03 +0530
> From: Ekta Jain <Ekta.Jain at teri.res.in>
> To: bioconductor at r-project.org
> Subject: [BioC] Average expression value from limma
>
> Dear Bioconductor Mailing List,
> I have a microarray data which i normalised using 'gcrma' followed by limma
> for Mock vs Treated, 3 replicates in each group. The 'topTable' returns an
> average expression value for each probeset. How is this exactly calculated?
>
> Also i compared this with the average expression of each probeset for all
> samples, such as
> (Embedded image moved to file: pic17982.gif)
>
> The 'Avg.Expr.from.limma' has a very high value as compared to the ones
> obtained from the normalised data. Is there anything wrong?
>
> Much appreciate any comments please.
>
> Regards,
> Ekta Jain
> Research Analyst
> Biotechnology and Bio-resources Division
> The Energy and Resources Institute, India Habitat Centre
> Lodhi Road, New Delhi - 110033
> #09958818853
> ekta.jain at teri.res.in
>

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