[BioC] limma

Peter Wilkinson pwilkinson at videotron.ca
Thu Jul 15 21:51:53 CEST 2004

Ah yes you are right I can type the function in. I would prefer to get the 
source code for the comments. The problem is that I did not notice where 
the source code resides. I have downloaded from the source link from the 
bioconductor site, and I will try that.

Thanks for your input.


At 10:44 AM 7/15/2004, James MacDonald wrote:
>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 ?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

More information about the Bioconductor mailing list