 
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 find
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 is
but I would still like to see it documented somewhere.
 
Can anyone point me to where topTable is further documented?
 
Thanks.
 
 
John Seers
 
 
My topTable looks like this:
 
 
> tt
               ID      logFC   AveExpr         t      P.Value  adj.P.Val
B
2258    201746_at  1.3663846  6.820456 10.128598 3.556998e-07 0.00851581
5.974622
6603    211074_at  1.3773921 10.003785  9.051149 1.166839e-06 0.01396765
5.134525

 
My topTable help only gives me this:

Value


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

genelist	 if genelist was included as input	
M	 estimate of the effect or the contrast, on the log2 scale	
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	
 
 
 
> sessionInfo()
R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 
 
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
 
attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
"datasets"  "utils"     "methods"   "base"     
 
other attached packages:
nugohs1a520180probe   nugohs1a520180cdf                samr
marray         geneplotter 
            "1.0.0"             "1.0.0"              "1.24"
"1.12.0"            "1.12.0" 
           annotate               gcrma         matchprobes
makecdfenv               limma 
           "1.12.1"             "2.6.0"             "1.6.0"
"1.12.0"            "2.9.13" 
               affy              affyio             Biobase
RWinEdt 
           "1.12.2"             "1.2.0"            "1.12.2"
"1.7-5" 
> 

 
 
 
 
 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

tel +44 (0)1603 251497
fax +44 (0)1603 507723
e-mail john.seers@bbsrc.ac.uk                         
e-disclaimer at http://www.ifr.ac.uk/edisclaimer/
<http://www.ifr.ac.uk/edisclaimer/>  
 
Web sites:

www.ifr.ac.uk <http://www.ifr.ac.uk/>    
www.foodandhealthnetwork.com <http://www.foodandhealthnetwork.com/> 
 

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