I saw there was discussion about smoothing after  CRMAv2 and before CBS 
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.


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