[BioC] Nimblegen data analysis

[Todd Richmond]

Hi Jenny,

I gave Benilton some example files for the oligo package - I haven't 
checked to see if they made it into the latest release. If they didn't 
make it in yet, I can see about making sure that some example files make 
it onto our website.

Regards, Todd


Jenny Drnevich wrote:
> 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
> 
> 
> 


-- 
Todd Richmond, PhD
Manager of Research Informatics
NimbleGen Systems, Inc
Madison, WI 53719
1-608-218-7600