Hi Henrik Thanks!! I understand. It seems X-files. I dont known what happens because i use the same script. May be the problem is related to past reruns in other computer (and probably other versions).
When i use the script in a new rawdata folder (moving the cels and thus no using probedata and other temporary directories) the results are the expected. Yes, i will check the pscbs vignette. Best Juanjo El martes, 15 de abril de 2014 18:43:42 UTC+2, Henrik Bengtsson escribió: > > 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...@ciberehd.org <javascript:>> 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-af...@googlegroups.com<javascript:> > > 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 <javascript:>. > > 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.
