What is the best aCGH normalization method for hyper-ploid tumor samples?

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9.3 years ago

sjorsvanheuveln ▴ 60

Hi people,

I'm currently working on aCGH data of Triple Negative Breast Cancer patients xenografts and primary tumor samples. A substantial amount of my samples is highly aberrated which leads to offsets of the diploid bands away from the log2ratio of 0.

I found an article on a prospective normalization for this: http://www.biomedcentral.com/1471-2164/8/382/ which includes the popLowess package in R: http://baseplugins.thep.lu.se/wiki/se.lu.onk.popLowess

However this a method from 2007 and I was wondering whether other approaches now exist that perhaps perform better (or different) aCGH normalizations. Ideas are very much welcome, thanks.

Greetings,
Sjors van Heuveln

hyperploid cancer normalization copy-number aCGH • 1.7k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by sjorsvanheuveln ▴ 60

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