[BioC] limma and files with separate channels
sdavis2 at mail.nih.gov
Fri Apr 29 16:54:08 CEST 2005
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
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
> into two respective files. So is there any way to read them without
> 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
>>> Each of my plates don't result in one file with the cy3 and cy5
>>> in it, but rather, each produces two files, one for each channel.
>>> 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
>> 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
>> format that is supported by the limma package.
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