Nimblegen data analysis
2
0
Entering edit mode
Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 9.6 years ago
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
GO cdf affy oligo GO cdf affy oligo • 912 views
ADD COMMENT
0
Entering edit mode
Todd Richmond ▴ 140
@todd-richmond-367
Last seen 9.6 years ago
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
ADD COMMENT
0
Entering edit mode
@jdelasherasedacuk-1189
Last seen 8.6 years ago
United Kingdom
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
ADD COMMENT

Login before adding your answer.

Traffic: 548 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6