[BioC] limma

Gordon K Smyth smyth at wehi.EDU.AU
Fri Jul 16 03:57:34 CEST 2004

Others have pointed out to you how to access the source code, but there is
no real need to make the modification to limma that you seeking to do. 
Instead of removing problem genes from the data set, simply assign them
weight zero.  This is exactly equivalent to removing them in the
normalization step but avoids having to re-index the sub-grids.


> 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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