Hi, from the script you attached I see that you're looking at the online vignette
http://aroma-project.org/vignettes/PairedPSCBS-lowlevel FYI, there is also a vignette in the PSCBS package [e.g. cran.r-project.org/web/packages/PSCBS] that you might find useful, particularly on how to avoid segment centromeres. On Tue, Apr 15, 2014 at 4:32 AM, Juan José Lozano Salvatella <juanjo.loz...@ciberehd.org> wrote: > Hi Henrik > > > when i run the two samples in a same directory ( a new (re) run without > others pairs) . The results are ok. This is not clear to me; are you saying that the script you attached solved the problem, but what you did before (not shown) does not work? If so, what did you do before? /Henrik > > > my details: > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] sfit_0.3.0 aroma.light_1.30.5 matrixStats_0.8.14 > [4] aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.8.2 > [7] R.filesets_2.4.0 R.utils_1.29.8 R.oo_1.18.0 > [10] affxparser_1.32.3 R.methodsS3_1.6.1 > > loaded via a namespace (and not attached): > [1] aroma.apd_0.5.0 base64enc_0.1-1 digest_0.6.4 DNAcopy_1.34.0 > [5] PSCBS_0.40.4 R.cache_0.9.0 R.huge_0.8.0 R.rsp_0.15.0 > [9] splines_3.0.1 tools_3.0.1 > > Any comments are wellcome! > > Thanks a lot > > Best > > Juanjo > > > > > El lunes, 14 de abril de 2014 23:51:20 UTC+2, Henrik Bengtsson escribió: >> >> Hi, >> >> agree, that certainly doesn't look correct - but there's probably a >> simple explanation/fix. Before anything else, what version of PSCBS >> are you running, i.e. what's your sessionInfo(). Also, exactly what >> does you script look like, and if you have a problematic sample you >> could share with me, that would help me reproduce this and help you. >> >> Cheers, >> >> Henrik >> >> On Mon, Apr 14, 2014 at 4:55 AM, Juan José Lozano Salvatella >> <juanjo...@ciberehd.org> wrote: >> > Hi >> > >> > I run the Vignette: Paired parent-specific copy-number segmentation >> > (Paired >> > PSCBS) and we obtain some segments as the attached file. >> > >> > CNV segments are diffcult to explain. Could you explain this? >> > >> > Thanks a lot in advance >> > >> > Best >> > >> > Juanjo >> > >> > -- >> > -- >> > 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/ >> > >> > --- >> > You received this message because you are subscribed to the Google >> > Groups >> > "aroma.affymetrix" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to aroma-affymetr...@googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
