Normalize breast cancer copy number variation profiles

Normalize breast cancer copy number variation profiles


In this video, I will demonstrate how to normalize copy number variation (or CNV) profiles. Specifically, those related to breast cancer samples. The inputs for this analysis are the files
we created in Genomica’s ModuleMap. First, launch GenePattern and search for the Acgh2Tab module. Once loaded, navigate to your local directory under the GenomeSpace tab, and drag the acgh text file into the input file parameter; the present list file into the present list file parameter; the absent list into the absent
file parameter; and, the genelocs file should read, “hg18”. Click “run” and once the job has finished,
save the converted acgh file, acgh.avergene.tab, to GenomeSpace as shown.

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