[BioC] Nimblegen data analysis
todd at nimblegen.com
Tue May 15 20:46:25 CEST 2007
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.
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...
> 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
>> > CEL files for further analysis.
>> > Can something similar be done with the Nimblegen data (given the FTR
>> > and the NDF file) for analysis?
>> > Thanks
>> > Dhruv
>> Todd Richmond, PhD
>> Manager of Research Informatics
>> NimbleGen Systems, Inc
>> Madison, WI 53719
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> Search the archives:
> 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
> 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
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