[BioC] Limma Documentation: normalization functions

Gordon Smyth smyth at wehi.edu.au
Sat Aug 9 19:09:22 MEST 2003

Dear Paul,

At 05:24 AM 9/08/2003, Paul Boutros wrote:
>Hi all,
>I'm trying to get familiar with the limma package, but I've run into 
>I don't understand.  After I load the package, if I type:
>The documentation doesn't give a list of available normalization methods.
>Instead it refers me to:
>"An overview of LIMMA functions for normalization is given in 

I have reproduced below the first few paragraphs of the help document that 
one gets by typing ?normalizeWithinArrays. As you can see, documentation 
for the argument "method" gives a list of available normalization methods. 
There are further details further down in the document under "Details". The 
line that you have quoted is the second last line of the help document. It 
would seem that you are only reading the last two lines of the document.

normalizeWithinArrays         package:limma         R Documentation

Normalize Within Arrays


      Normalize the expression log-ratios for one or more two-colour
      spotted microarray experiments so that the log-ratios average to
      zero within each array or sub-array.


      normalizeWithinArrays(object, layout, method="printtiploess", 
weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5, 


   object: object of class `list', `RGList' or `MAList' containing
           two-color microarray data

   layout: list specifying the dimensions of the spot matrix and the
           grid matrix

   method: character string specifying the normalization method. Choices
           are `"none"', `"median"', `"loess"', `"printtiploess"',
           `"composite"' and `"robustspline"'. A partial string
           sufficient to uniquely identify the choice is permitted. If
           no method is recognized, then unnormalized M and A-values are
------------------ rest of document deleted -------------------

>However, when I go to the "limma: Linear Models for Microarray Data User's
>Guide" (a pdf in the limma folder of my /library) there is no section on
>normalization there.  I also didn't see a vignette for limma.

The User's Guide is the vignette for LIMMA. Although there isn't a separate 
section on normalization, there are four complete data case studies all of 
which include commands for normalization.

>  Since nobody
>else has asked about this, I figure the documentation is here somewhere, 
>and I
>just don't know where to find it!  Any guidance much appreciated.
>limma user's Guide is 19-May-2003.
>limma is 1.0.8

It might be a good idea to install the development version of limma which 
is up to version 1.1.10. The html version of the User's Guide is also 
updated somewhat in the development version.


>R is 1.7.1
>OS is WinXP SP1

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