[BioC] Limma Documentation: normalization functions
Paul.Boutros at utoronto.ca
Sat Aug 9 15:38:47 MEST 2003
> -----Original Message-----
> From: Gordon Smyth [mailto:smyth at wehi.edu.au]
> Sent: Saturday, August 09, 2003 4:09 AM
> To: Paul.Boutros at utoronto.ca
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Limma Documentation: normalization functions
> 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
> 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 -------------------
This is weird: I get totally different output. I've appended mine below.
Is this just a version issue, or is it something I should worry about?
------------------ Begin document ------------------------------
normalizeWithinArrays package:limma R Documentation
Normalize Within Arrays - generic
A generic function which normalizes microarray data. Normalization
is intended to remove from the expression measures any systematic
trends which arise from the microarray technology rather than from
differences between the probes or between the target RNA samples
hybridized to the arrays.
object: a data object containing microarray data
...: any other arguments
Methods are defined in limma for `object' an object of class
`list', `RGList' or `MAList'.
Type `showMethods("normalizeBetweenArrays")' at the R prompt for a
complete list of classes for which methods are defined.
An overview of LIMMA functions for normalization is given in
See also `normalizeBetweenArrays' and `maNorm' in the marrayNorm
------------------ End document --------------------------------
> >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.
Okay, will do. Thanks!
> >R is 1.7.1
> >OS is WinXP SP1
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