Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions
Just a follow up on this thread and close it: Starting with aroma.core v1.8.0 (2010-11-07) it is possible to specify additional parameters when setting up the segmentation model, parameters that will be passed to the actual segmentation method. For instance, (instead of having to pass them as arguments to fit(), the preferred way is now to do: seg - CbsModel(ds, min.width=5); fit(seg); This means that also: seg - CbsModel(ds, min.width=5); ce - ChromosomeExplorer(seg); process(seg); will also work (where fit() is called implicitly by process()). Note that the aroma framework only pass on these optional arguments to the underlying segmentation method. In order to find out which they are and what they do, see the specific segmentation method, e.g. help(segment, package=DNAcopy). /Henrik On Wed, Sep 29, 2010 at 8:20 PM, Dario Strbenac d.strbe...@garvan.org.au wrote: 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=vertebrateorg=Humandb=hg18position=chr1%3A0-16430583 2 1 14944039 16878322 -0.3535 1163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A14750611-17071750 3 1 16878364 17215511 -0.0717 163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16844649-17249226 4 1 17217671 26830062 -0.3424 6070 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16256432-27791301 5 1 26830481 72541505 0.1856 28889 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A22259379-77112607 6 1 72541525 72583737 2.0660 45 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A72537304-72587958 7 1 72584492 101046159 0.1900 18772 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A69738325-103892326 8 1 101046857 101047369 -2.8866 2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A101046806-101047420 9 1 101047606 150822152 0.1841 15874 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A96070151-155799607 10 1 150822331 150852863 2.6550 31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=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
Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions
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=vertebrateorg=Humandb=hg18position=chr1%3A0-16430583 2 1 14944039 16878322 -0.3535 1163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A14750611-17071750 3 1 16878364 17215511 -0.0717 163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16844649-17249226 4 1 17217671 26830062 -0.3424 6070 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16256432-27791301 5 1 26830481 72541505 0.1856 28889 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A22259379-77112607 6 1 72541525 72583737 2.0660 45 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A72537304-72587958 7 1 72584492 101046159 0.1900 18772 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A69738325-103892326 8 1 101046857 101047369 -2.8866 2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A101046806-101047420 9 1 101047606 150822152 0.1841 15874 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A96070151-155799607 10 1 150822331 150852863 2.6550 31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=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/
Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions
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=vertebrateorg=Humandb=hg18position=chr1%3A0-16430583 2 1 14944039 16878322 -0.3535 1163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A14750611-17071750 3 1 16878364 17215511 -0.0717 163 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16844649-17249226 4 1 17217671 26830062 -0.3424 6070 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A16256432-27791301 5 1 26830481 72541505 0.1856 28889 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A22259379-77112607 6 1 72541525 72583737 2.0660 45 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A72537304-72587958 7 1 72584492 101046159 0.1900 18772 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A69738325-103892326 8 1 101046857 101047369 -2.8866 2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A101046806-101047420 9 1 101047606 150822152 0.1841 15874 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A96070151-155799607 10 1 150822331 150852863 2.6550 31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=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
