[BioC] Nimblegen data analysis

[J.delasHeras at ed.ac.uk]

Hi Jenny,

You might want to take a look at the package 'Ringo' as well, which is  
designed specifically for Nimblegen format data and uses limma... I  
haven't yet done much more than installing it, but it looks good.

Jose

Quoting Jenny Drnevich <drnevich at uiuc.edu>:

> Hi Todd,
>
> Are there any publicly-available NimbleGen XYS and NDF files that I
> could get my hands on to practice analyzing? Public repositories like
> GEO don't have the original files, from what I've been able to tell...
>
> Thanks,
> Jenny
>
> At 09:29 AM 4/18/2007, Todd Richmond wrote:
>> Hi Dhruv,
>>
>> You probably want to take a look at the oligo package
>> (http://bioconductor.org/packages/2.0/bioc/html/oligo.html), which reads
>> NimbleGen XYS and NDF files. That will get your data into some standard
>> data objects and you can go from there.
>>
>> Regards, Todd
>>
>> dhruv pant wrote:
>> > Hi,
>> > I had a question regarding reading Nimblegen chip data ('FTR' files,
>> > probably the equivalent of CEL files)
>> >  and doing model fitting etc (fitPLM) in R.
>> > For Affy chips, to do this, one needs the CDF files for the chip and the
>> > CEL files for further analysis.
>> >
>> > Can something similar be done with the Nimblegen data (given the FTR files
>> > and the NDF file)  for analysis?
>> >
>> >
>> > Thanks
>> > Dhruv
>> >
>>
>>
>> --
>> Todd Richmond, PhD
>> Manager of Research Informatics
>> NimbleGen Systems, Inc
>> Madison, WI 53719
>> 1-608-218-7600
>>
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>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
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>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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