[BioC] limma and files with separate channels

[Guoneng Zhong]

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.

Thanks,
G