[BioC] limma and files with separate channels

[Gordon Smyth]

>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