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
>something
>I don't understand. After I load the package, if I type:
>?normalizeWithinArrays
>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
>4.Normalization."
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
Description:
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.
Usage:
normalizeWithinArrays(object, layout, method="printtiploess",
weights=object$weights, span=0.3, iterations=4, controlspots=NULL, df=5,
robust="M")
MA.RG(object)
Arguments:
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
returned.
------------------ 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.
>
>Paul
>
>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.
Regards
Gordon
>R is 1.7.1
>OS is WinXP SP1