[BioC] limma and files with separate channels

[Sean Davis]

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 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
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor