Re: [aroma.affymetrix] Paired total copy-number analysis
Good morning, Il giorno giovedì 27 settembre 2012 22:02:48 UTC+2, Henrik Bengtsson ha scritto: Hi. On Thu, Sep 27, 2012 at 6:36 AM, Martina Dori martin...@gmail.comjavascript: wrote: Hi Henrik, after managing to install and run correctly aroma package, I ran the Paired total copy number analysis CRMAv2 (It's the first time, so I strictly followed the vignette). Sounds like a good strategy. At the end when trying to display the results # Link the ChromosomeExplorer to the segmentation model ce - ChromosomeExplorer(cns); print(ce); # Fit the model for a few chromosomes process(ce, chromosomes=c(12, 13, 17), verbose=verbose); R crushed because of the wrong version of Xcode (I have already installed the latest one); If you can reproduce it and report the details on what's happening, I/we might be able to help you. Also, does R really crash (=abruptly quits), or does it give a regular R error (so you can continue later)? R quit and an error window popped out saying that the right X code was missing (that's why I knew that was the problem and fixed it immediately). I tried to look for the cbs final report in my working directory, but I wasn't able to find it. At the end, process() for ChromosomeExplorer will write a regions.xls file to the reports/data set/tags/cbs/ directory. However, if it crashed/gives an error, this will obviously not be reached. You can always do this manually, pathname - writeRegions(ce, chromosomes=c(12,13,17), verbose=verbose); print(pathname); # = This will let you know where the regions.xls file is located. Ok, I will keep this in mind! Do I have to run again all the code and add a particular command at the end for saving the output, or is it just that it has been saved somewhere else? The philosophy of the Aroma Framework is that all intermediate and final results are stored to the file system. This, means that if you rerun the same script again, what is already processed will be skipped more or less instantaneously. /Henrik That's really a great idea you had when developing the aroma package! And this lets me breathe again a little bit! Thank you very much for your help! Martina Thank you very much for your patience! Martina Il giorno lunedì 24 settembre 2012 19:55:51 UTC+2, Henrik Bengtsson ha scritto: On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen clausli...@gmail.com wrote: Hi, Last week I ran CRMA (v2): Paired total copy number analysis Using the following annotation files GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,HB20080710.acs The script ran without any problems. But I am a little uncertain about whether the output is mapped to hg18 or hg19 ? As the annotation files are hg19 I expected the output to be so, too. But in the outfile from CBS regions.xls all entries are associated url of this format http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A32255-386024 Indicating that the mapping is to hg18.? Can anyone explain ? Don't worry, everything in your analysis is correct. It's just that the file generated by CbsModel has hg18 hard wired in the output. You can manually search-and-replace hg18 and hg19 and everything should be as you expected. /Henrik Help will be much appreciated !! Claus -- 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-af...@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-af...@googlegroups.comjavascript: 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
Re: [aroma.affymetrix] Paired total copy-number analysis
Hi Henrik, after managing to install and run correctly aroma package, I ran the Paired total copy number analysis CRMAv2 (It's the first time, so I strictly followed the vignette). At the end when trying to display the results # Link the ChromosomeExplorer to the segmentation model ce - ChromosomeExplorer(cns); print(ce); # Fit the model for a few chromosomes process(ce, chromosomes=c(12, 13, 17), verbose=verbose); R crushed because of the wrong version of Xcode (I have already installed the latest one); I tried to look for the cbs final report in my working directory, but I wasn't able to find it. Do I have to run again all the code and add a particular command at the end for saving the output, or is it just that it has been saved somewhere else? Thank you very much for your patience! Martina Il giorno lunedì 24 settembre 2012 19:55:51 UTC+2, Henrik Bengtsson ha scritto: On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen clausli...@gmail.com javascript: wrote: Hi, Last week I ran CRMA (v2): Paired total copy number analysis Using the following annotation files GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,HB20080710.acs The script ran without any problems. But I am a little uncertain about whether the output is mapped to hg18 or hg19 ? As the annotation files are hg19 I expected the output to be so, too. But in the outfile from CBS regions.xls all entries are associated url of this format http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A32255-386024 Indicating that the mapping is to hg18.? Can anyone explain ? Don't worry, everything in your analysis is correct. It's just that the file generated by CbsModel has hg18 hard wired in the output. You can manually search-and-replace hg18 and hg19 and everything should be as you expected. /Henrik Help will be much appreciated !! Claus -- 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-af...@googlegroups.comjavascript: 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] Paired total copy-number analysis
Hi. On Thu, Sep 27, 2012 at 6:36 AM, Martina Dori martina.d...@gmail.com wrote: Hi Henrik, after managing to install and run correctly aroma package, I ran the Paired total copy number analysis CRMAv2 (It's the first time, so I strictly followed the vignette). Sounds like a good strategy. At the end when trying to display the results # Link the ChromosomeExplorer to the segmentation model ce - ChromosomeExplorer(cns); print(ce); # Fit the model for a few chromosomes process(ce, chromosomes=c(12, 13, 17), verbose=verbose); R crushed because of the wrong version of Xcode (I have already installed the latest one); If you can reproduce it and report the details on what's happening, I/we might be able to help you. Also, does R really crash (=abruptly quits), or does it give a regular R error (so you can continue later)? I tried to look for the cbs final report in my working directory, but I wasn't able to find it. At the end, process() for ChromosomeExplorer will write a regions.xls file to the reports/data set/tags/cbs/ directory. However, if it crashed/gives an error, this will obviously not be reached. You can always do this manually, pathname - writeRegions(ce, chromosomes=c(12,13,17), verbose=verbose); print(pathname); # = This will let you know where the regions.xls file is located. Do I have to run again all the code and add a particular command at the end for saving the output, or is it just that it has been saved somewhere else? The philosophy of the Aroma Framework is that all intermediate and final results are stored to the file system. This, means that if you rerun the same script again, what is already processed will be skipped more or less instantaneously. /Henrik Thank you very much for your patience! Martina Il giorno lunedì 24 settembre 2012 19:55:51 UTC+2, Henrik Bengtsson ha scritto: On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen clausli...@gmail.com wrote: Hi, Last week I ran CRMA (v2): Paired total copy number analysis Using the following annotation files GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,HB20080710.acs The script ran without any problems. But I am a little uncertain about whether the output is mapped to hg18 or hg19 ? As the annotation files are hg19 I expected the output to be so, too. But in the outfile from CBS regions.xls all entries are associated url of this format http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A32255-386024 Indicating that the mapping is to hg18.? Can anyone explain ? Don't worry, everything in your analysis is correct. It's just that the file generated by CbsModel has hg18 hard wired in the output. You can manually search-and-replace hg18 and hg19 and everything should be as you expected. /Henrik Help will be much appreciated !! Claus -- 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-af...@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/ -- 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] Paired total copy-number analysis
On Mon, Sep 24, 2012 at 5:55 AM, tClaus Lindbjerg Andersen clauslindbj...@gmail.com wrote: Hi, Last week I ran CRMA (v2): Paired total copy number analysis Using the following annotation files GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,HB20080710.acs The script ran without any problems. But I am a little uncertain about whether the output is mapped to hg18 or hg19 ? As the annotation files are hg19 I expected the output to be so, too. But in the outfile from CBS regions.xls all entries are associated url of this format http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrateorg=Humandb=hg18position=chr1%3A32255-386024 Indicating that the mapping is to hg18.? Can anyone explain ? Don't worry, everything in your analysis is correct. It's just that the file generated by CbsModel has hg18 hard wired in the output. You can manually search-and-replace hg18 and hg19 and everything should be as you expected. /Henrik Help will be much appreciated !! Claus -- 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/
