[BioC] Nimblegen data analysis

Jenny Drnevich drnevich at uiuc.edu
Tue May 15 17:44:06 CEST 2007

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 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
>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
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e-mail: drnevich at uiuc.edu

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