Thanks for this. ---- Original message ---- >Date: Wed, 29 Sep 2010 20:14:03 -0700 >From: aroma-affymetrix@googlegroups.com (on behalf of Henrik Bengtsson ><h...@aroma-project.org>) >Subject: Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions >To: aroma-affymetrix <aroma-affymetrix@googlegroups.com> > >Hi. > >On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac ><d.strbe...@garvan.org.au> wrote: >> Hello, >> >> I remember reading a while ago that you can pass in additional parameters to >> CbsModel, and they will get passed onto DNAcopy functions. However, it >> doesn't seem to be working for me. I don't want any segments less than 5 >> probes wide. However, the 8th segment is only 2 wide. >> >>> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2), >>> min.width = 5) >>> fit(model, force = TRUE) > >Your expectation that you should specify the extra parameters in the >setup of the CbsModel object follows the overall style of the aroma >framework. However, in this particular case we haven't implemented >passing parameters that way. However, a workaround is to do it via >the fit() call instead. In your case, you would do: > >model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2)); >fit(model, min.width=5, force=TRUE); > >Hope this helps > >Henrik > >> There were 50 or more warnings (use warnings() to see the first 50) >>> foldChangeTable <- getRegions(model)[[1]] >>> foldChangeTable[1:10,] >> chromosome start stop mean count >> >> url >> 1 1 51599 14941584 0.1975 7929 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583 >> 2 1 14944039 16878322 -0.3535 1163 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750 >> 3 1 16878364 17215511 -0.0717 163 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226 >> 4 1 17217671 26830062 -0.3424 6070 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301 >> 5 1 26830481 72541505 0.1856 28889 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607 >> 6 1 72541525 72583737 2.0660 45 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958 >> 7 1 72584492 101046159 0.1900 18772 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326 >> 8 1 101046857 101047369 -2.8866 2 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420 >> 9 1 101047606 150822152 0.1841 15874 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607 >> 10 1 150822331 150852863 2.6550 31 >> http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916 >> >> I don't think the warnings are related to my question, but here they are, >> anyway : >> >>> warnings() >> Warning messages: >> 1: In log(M, base = 2) : NaNs produced >> 2: In log(A, base = 2) : NaNs produced >> 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : >> array has repeated maploc positions >> >> 4: In log(M, base = 2) : NaNs produced >> 5: In log(A, base = 2) : NaNs produced >> 6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome, ... : >> array has repeated maploc positions >> ... ... ... >> >> I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha. >> >> -------------------------------------- >> Dario Strbenac >> Research Assistant >> Cancer Epigenetics >> Garvan Institute of Medical Research >> Darlinghurst NSW 2010 >> Australia >> >> -- >> When reporting problems on aroma.affymetrix, make sure 1) to run the latest >> version of the package, 2) to report the output of sessionInfo() and >> traceback(), and 3) to post a complete code example. >> >> >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group with website http://www.aroma-project.org/. >> To post to this group, send email to aroma-affymetrix@googlegroups.com >> To unsubscribe and other options, go to http://www.aroma-project.org/forum/ >> > >-- >When reporting problems on aroma.affymetrix, make sure 1) to run the latest >version of the package, 2) to report the output of sessionInfo() and >traceback(), and 3) to post a complete code example. > > >You received this message because you are subscribed to the Google Groups >"aroma.affymetrix" group with website http://www.aroma-project.org/. >To post to this group, send email to aroma-affymetrix@googlegroups.com >To unsubscribe and other options, go to http://www.aroma-project.org/forum/
-------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
