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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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

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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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

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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- 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 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK