[BioC] limma

Peter Wilkinson pwilkinson at videotron.ca
Fri Jul 16 06:22:58 CEST 2004

Hi there,

Thank you for your input. In fact this morning I tried just that, setting 
the gene to 0, and I found that to work.


At 09:57 PM 7/15/2004, Gordon K Smyth wrote:
>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

More information about the Bioconductor mailing list