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List:       bioconductor
Subject:    [BioC] Calculating average expression value in limma topTable output
From:       Michael Muratet <mmuratet () hudsonalpha ! org>
Date:       2010-11-30 19:40:12
Message-ID: 4807DE44-0098-4AE3-B5B0-C6E990929F39 () hudsonalpha ! org
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Dear Colleagues

I have a question about how the AveExpr value gets calculated in limma  
topTable. Actually, it appears to get calculated in lmFit, e.g.,

from lmFit:
$Amean
uc007aet.1 uc007aeu.1 uc007aev.1 uc007aew.1 uc007aex.1
  0.8269211  1.1462191 -2.3369824 -6.0639390 -8.4696942

from topTable:
acomps.txt:uc007aet.1 -1.07454088439694 0.826921104052945  
-0.83217169279942 0.413619779606768 0.999993313025155 -5.09985857376248
bcomps.txt:uc007aet.1 -0.590082310688743 0.826921104052945  
-0.559690866321207 0.580942531774888 0.999999437256152 -4.75598562188099

So AveExpr = Amean

But I have looked at the 'average log-intensity' for the raw values  
and for the fitted coefficients for log10, log2 and log and looked at  
mean(log(x)) and log(mean(x)) and I can't get 0.8269211. I can post  
the data if need be.

Moreover, many of the fitted coefficients are less than zero and  
log(mean(x)) is defined but not mean(log(x)).

Can anyone tell me how Amean (and therefore AveExpr) gets calculated?

Thanks

Mike



Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet@hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806

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