[BioC] limma and files with separate channels

Guoneng Zhong guoneng.zhong at yale.edu
Fri Apr 29 15:47:20 CEST 2005

No, I don't think it is ImaGene.  We have high density Nimblegen arrays we get
from NASA, and NASA, for traditional reasons, reads the two channels separately
into two respective files.  So is there any way to read them without actually
modifying the image results files?



Systems Programmer
Yale Center for Medical Informatics
fax: 203-737-5708

Quoting Gordon Smyth <smyth at wehi.edu.au>:

> >Date: Thu, 28 Apr 2005 16:34:36 -0400
> >From: Guoneng Zhong <guoneng.zhong at yale.edu>
> >Subject: [BioC] limma and  files with separate channels
> >To: bioconductor at stat.math.ethz.ch
> >
> >Hi,
> >
> >Each of my plates don't result in one file with the cy3 and cy5 channels
> >in it, but rather, each produces two files, one for each channel.  How
> >could I construct the target file for something very basic like a
> >reference design without having to merge the pair of files first.
> Is it possible that you are using ImaGene, which does write separate files
> for Cy3 and Cy5? See page 8 of the Limma User's Guide
> (http://bioinf.wehi.edu.au/limma/usersguide.pdf) for an example of a
> targets file in this situation.
> ImaGene is the only image analysis program that we know of that writes
> separate files for Cy3 and Cy5, and therefore is the only separate-file
> format that is supported by the limma package.
> Gordon
> >Thanks,
> >G

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