Scripts to handle array CGH data files from NimbleGen
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Todd Richmond ▴ 140
@todd-richmond-367
Last seen 7.1 years ago
Hi Romain, I have some preliminary code which reads in NimbleGen CGH ratio files, passes it to tilingArray, and produces plots and tables identical to our deliverables. It still needs a bit more work and testing but I should have that ready sometime next week. I'll send you an email when it's ready. Todd rdesprat wrote: > Dear Todd, > > > > I am trying to use Tilling array for my CGH data from nimblegen but I don' > succeed. Would you have something written down about how to do it ? > > > > > > Romain Desprat > > > > PhD student > > Albert Einstein Medical School (NY) > > rdesprat at aecom.yu.edu > > 7184303119 > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > -- Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc Madison, WI 53719 1-608-218-7600
CGH tilingArray CGH tilingArray • 610 views
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@ma3mlsbathacuk-1865
Last seen 7.1 years ago
Hi Romain The package snapCGH also has functionality for reading of Nimblegen aCGH data, and provides preprocessing methods from within itself and the package limma, as well as use of the segmentation method from tilingArray (although not much of the other functionality from tilingArray). Mike Smith Quoting Todd Richmond <todd at="" nimblegen.com="">: > Hi Romain, > > I have some preliminary code which reads in NimbleGen CGH ratio files, > passes it to tilingArray, and produces plots and tables identical to our > deliverables. It still needs a bit more work and testing but I should > have that ready sometime next week. I'll send you an email when it's ready. > > Todd > > > rdesprat wrote: >> Dear Todd, >> >> >> >> I am trying to use Tilling array for my CGH data from nimblegen but I don' >> succeed. Would you have something written down about how to do it ? >> >> >> >> >> >> Romain Desprat >> >> >> >> PhD student >> >> Albert Einstein Medical School (NY) >> >> rdesprat at aecom.yu.edu >> >> 7184303119 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> >> > > > -- > 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 >
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