[BioC] limma

James MacDonald jmacdon at med.umich.edu
Thu Jul 15 16:44:04 CEST 2004

The code is available to you right now. The easiest way to get it is to
type normalizeWithinArrays at an R prompt, copy and paste into your
favorite editor. If you want the source code with any comments that may
exist, you will have to download the source version of limma, untar and
gunzip it and then open norm.R in your favorite editor.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Peter Wilkinson <pwilkinson at videotron.ca> 07/14/04 05:36PM >>>
Hi there,

I would like to explore the idea of creating a function that is 
a  modification of the normalizeWithinArrays() with printtiploess
option of 
the limma package.

We are spot quality control prior to normalization which results in
genes being dropped. Once that happens then we no longer have complete

sub-grids; normlizeWithinArrays will nor longer work with the printtip

loess option. So I wish to make a modification to the
function that will re-index each sub-grid, so that the print top loess
be performed.

So I have been looking for the source code for limma, but it seams to
unavailable since the package is distributed as a binary. I have
the author's page but its not there either.

I would like permission to look into the limma package source code and

re-factor the normalizeWithinArrays() function to do what I want.

Can somebody send me the source code ?


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