Re: [aroma.affymetrix] Doubts in PSCBS segments
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-8LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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.comjavascript: 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.
Re: [aroma.affymetrix] Doubts in PSCBS segments
On Wed, Apr 16, 2014 at 5:44 AM, Juan José Lozano Salvatella juanjo.loz...@ciberehd.org wrote: 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). I'm sure there are no aliens or higher powers involved; instead there's probably a very simple answer to this. 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. The way I read this is that you are forcing a new AS-CRMAv2 run. Since AS-CRMAv2 is completely deterministic, I don't see how this makes a difference. I still also don't understand if you are saying whether this solved your problem? Can you still reproduce the original problem or is appearing randomly? Looking at your two (Chr20) plots that you've sent, 'double_problem_cnv.png' and 'file_corrected.png' it doesn't look like to raw data is the same. So, to simplify your life, you could start by asserting that you get the exact same 'data' object when you rerun AS-CRMAv2. If that is not the case, the problem is unrelated to PSCBS and that should be troubleshooted first. I would save 'data' after these steps: data - extractPSCNArray(res$total); dimnames(data)[[3]] - names(pair); saveObject(data, data-run1.Rbin) then re-run in a different directory and save as: saveObject(data, data-run2.Rbin) then you can compare the two outputs: library(R.utils) data1 - loadObject(data-run1.Rbin) data2 - loadObject(data-run2.Rbin) stopifnot(all.equal(data1, data2)) As a I said above, I would be surprised if you don't get that 'data1' and 'data2' are equal/identical. /Henrik 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 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-8LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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
Re: [aroma.affymetrix] Doubts in PSCBS segments
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-8LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=es_ES.UTF-8LC_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_2.4.0R.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_0.6.4DNAcopy_1.34.0 [5] PSCBS_0.40.4R.cache_0.9.0 R.huge_0.8.0R.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
[aroma.affymetrix] Doubts in PSCBS segments
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-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. attachment: doubt_problem_cnv.png
