You may have to write your own parser. Alternatively, you can add an option to the read.maImages function to read the array files. I find the latter technique pretty useful, as then you can learn from Gordon's code. Sean On Apr 29, 2005, at 9:47 AM, Guoneng Zhong wrote: > 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? > > Thanks, > G > > > -- > > Systems Programmer > Yale Center for Medical Informatics > fax: 203-737-5708 > > > > Quoting Gordon Smyth <smyth@wehi.edu.au>: > >> >>> Date: Thu, 28 Apr 2005 16:34:36 -0400 >>> From: Guoneng Zhong <guoneng.zhong@yale.edu> >>> Subject: [BioC] limma and files with separate channels >>> To: bioconductor@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 >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor