[BioC] Limma Documentation: normalization functions

[Paul Boutros]

Hi Sir,

> -----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
> >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 -------------------

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

Description:

     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.

Usage:

     normalizeWithinArrays(object,...)

Arguments:

  object: a data object containing microarray data

     ...: any other arguments

Methods:

     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.

Author(s):

     Gordon Smyth

See Also:

     An overview of LIMMA functions for normalization is given in
     4.Normalization.

     See also `normalizeBetweenArrays' and `maNorm' in the marrayNorm
     package.
------------------ 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.
> >
> >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.

Okay, will do.  Thanks!
Paul

> Regards
> Gordon
>
> >R is 1.7.1
> >OS is WinXP SP1