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 > <[email protected]<javascript:>> > 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 > >> <[email protected]> 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 [email protected] > >> > 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 > > [email protected]<javascript:> > > 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
