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Old 07-21-2014, 04:06 PM   #42
arcolombo698
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Location: Los Angeles

Join Date: Nov 2013
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I am not a CGH expert by any means whatsoever. From my experiments, the germline samples are the controls, which are tumor free. The tumor samples have tumors, and we are measuring the variation between the two.

My best advice, is to go onto PubMed and find experiments similar to you. It depends on your experiment design and hypothesis. I am under the impression that the reference is the control. I am also not an expert with chicken experiments, I have only worked on hg19, and mm10 for NBL, and Medullo.

if you use the layer as the reference, the CNV data that will be output is in relation to the broiler changes with respect to layer. This just depends on your experiment design.
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