[BioC] limma topTable values

john seers (IFR) john.seers at bbsrc.ac.uk
Mon Apr 2 14:25:23 CEST 2007

Thanks Sean. That has fixed it. 

I thought I was up to date with limma but a new version has crept in
when I wasn't looking.

John Seers


John Seers
Institute of Food Research
Norwich Research Park

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-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 02 April 2007 13:03
To: bioconductor at stat.math.ethz.ch
Cc: john seers (IFR)
Subject: Re: [BioC] limma topTable values

On Monday 02 April 2007 07:38, john seers (IFR) wrote:
> Dear Bioconductor users
> I am using limma to analyse some Affymetrix arrays. (First time I have
> analysed Affymetrix ...)
> When I use "topTable" it returns a format that I have not seen before.
> If I enter "?topTable" the help text does not describe this format in
> the "Values" section. I have looked in the user manual but I cannot
> any information and I have generally searched but I cannot find a
> description of this format of topTable. Particularly I would like to
> know what AveExpr is and how it is calculated. I can guess what logFC
> but I would still like to see it documented somewhere.

An update to a newer version of limma will fix the issue.  From version 


     A dataframe with a row for the 'number' top genes and the
     following columns:

genelist: if genelist was included as input

   logFC: estimate of the log2-fold-change corresponding to the effect
          or contrast

 AveExpr: average log2-expression for the probe over all arrays and
          channels, same as 'Amean' in the 'MarrayLM' object

       t: moderated t-statistic

 P.Value: raw p-value

adj.P.Value: adjusted p-value or q-value

       B: log odds that the gene is differentially expressed


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