Differential copy number analysis

Question

[foreverlearner]

Similar to differential expression calculations across case/control with multiple samples, is there a way to find statistically significant "differential copy number" regions?

For example, if we know copy number for each sample for locus L in two cohorts (N1 cases and N2 controls), is there some difference in mean or something similar like statistic? Of course, with multiple testing corrections possibilities when interrogating 1000s of loci?

Answer 1

[Christian]

For microarrays, have a look at cn.FARMS, which I think can do that.

[foreverlearner]

Thanks Christian ... but I am looking for aCGH based analyses not SNPs.

[Christian]

I see. Please edit your question to make this clear.