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=vertebrate&org=Human&db=hg18&position=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/
