Hi. 1. It is not clear to me if you're saying that you get different results now using a newer version of aroma.affymetrix that you used before and on the same exact same data set, or something else. Nothing intentionally have changed in the CRMAv2 pipeline (and I cannot recall any recent updates at all to that pipeline), so if it "recently" started to "fail", it is most likely your data that is different now than what you used before.
2. It is not clear to me if you used CRMAv2 data for the "broad institute pipeline" or if that is a completely different pipeline. I also don't know what "broad institute pipeline" is. Is it using CBS for segmentation, or something else etc etc. 3. I don't know what I'm looking at in Picture1.png. /Henrik On Tue, Dec 17, 2013 at 8:47 PM, wisekh6 <wise...@gmail.com> wrote: > Dear Henrik, > > I had been using CRMAv2 many times to generate segmented copy numbers from > "Paired total copy-number analysis" using CRMAv2 with affymetrix snp6, and > all of my trials were successful. > Recently, however, this approach failed to generate a reasonable number of > segments, while an alternative way (using broad institute pipeline) worked > well, as shown in the attached. > I wonder if you can have a chance to examine this difference with any > intermediate file that CRMAv2 generated. > If you let me know which file you need, please let me know. > thank you in advance. > > Kim > > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] aroma.light_1.30.5 matrixStats_0.8.12 aroma.affymetrix_2.11.1 > [4] affxparser_1.32.3 aroma.core_2.11.0 R.devices_2.7.2 > [7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8 > [10] R.methodsS3_1.5.2 > > loaded via a namespace (and not attached): > [1] aroma.apd_0.4.0 digest_0.6.4 DNAcopy_1.34.0 PSCBS_0.40.2 > [5] R.cache_0.9.0 R.huge_0.6.0 R.rsp_0.9.28 tools_3.0.1 > > -- > -- > 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/groups/opt_out. -- -- 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/groups/opt_out.
