[BioC] limma

Kasper Daniel Hansen k.hansen at biostat.ku.dk
Thu Jul 15 23:27:38 CEST 2004

On Thu, Jul 15, 2004 at 03:51:53PM -0400, Peter Wilkinson wrote:
> 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.

R packages are basically distributed in two formats: source and binary. 
Unix versions are always source and windows are always binary. As long 
as you are only interested in the R code, you can - as James said - 
always get the source from within R (although it might be difficult 
depending on what function you want access to. "getAnywhere()" is nice 
to know about"). I think (99% sure) that you cannot get the C code from 
within R. The thing to do is retriving the source tarballs. Eg. getting 
the  source code for biobase may be done by pointing your webbrowser 
at "www.bioconductor.org" , click "devel packages", "biobase" and 
finally "source package download". Standard R packages may be gotten 
from CRAN in a similar fashion.

But if you are simply looking for the R code, the thing to do is 
probably accesing it through R.


> 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.
> >
> >HTH,
> >
> >Jim
> >
> >
> >
> >James W. MacDonald
> >Affymetrix and cDNA Microarray Core
> >University of Michigan Cancer Center
> >1500 E. Medical Center Drive
> >7410 CCGC
> >Ann Arbor MI 48109
> >734-647-5623
> >
> >>>> 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
> >some
> >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
> >normalizeWithinArrays
> >function that will re-index each sub-grid, so that the print top loess
> >can
> >be performed.
> >
> >So I have been looking for the source code for limma, but it seams to
> >be
> >unavailable since the package is distributed as a binary. I have
> >checked
> >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 ?
> >
> >Peter
> >
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Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen

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