Hi, I saw there was discussion about smoothing after CRMAv2 and before CBS (https://groups.google.com/forum/#!topic/aroma-affymetrix/DUquhAMhEuY). Henrik mentioned that function dropSegmentationOutliers in PSCBS can be used to drop TCN outliers. I am using CytoscanHD array which includes 750,000 SNP and 2.6 million copy number markers. I think CytoScanHD array can afford dropping some outliers.
My questions are, 1. Is it possible to drop outliers for TCN which were computed from total copy number and allelic-specific probes? As far as I know PSCBS is designed for allelic-specific probes. 2. If PSCBS works for my case where TCN is from total copy number estimates including allelic-specific probes, how to prepare for the input for PSCBS from the step after calling doCRMAv2 or exportTotalCnRatioSet? and how to make output from PSCBS to make aroma read and segment the data. Regarding to downstream analysis after segmentation, 1. Do you guys have any suggestions for copy number calling? How to decide which regions are amplified and deleted? 2. Do you know how to remove copy number polymorphism after segmentation. I am working cancer? I am more interested in copy number alterations. All comments are appreciated. Thanks. Br, C.Y -- -- 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 firstname.lastname@example.org 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.