Question: Differential copy number analysis
0
gravatar for foreverlearner
3.4 years ago by
United States
foreverlearner0 wrote:

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?

cgh • 1.0k views
ADD COMMENTlink modified 9 weeks ago by Biostar ♦♦ 20 • written 3.4 years ago by foreverlearner0

 

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

ADD REPLYlink written 3.4 years ago by foreverlearner0
I see. Please edit your question to make this clear.
ADD REPLYlink written 3.4 years ago by Christian2.6k
0
gravatar for Christian
3.4 years ago by
Christian2.6k
Cambridge, US
Christian2.6k wrote:
For microarrays, have a look at cn.FARMS, which I think can do that. http://www.bioconductor.org/packages/release/bioc/html/cn.farms.html
ADD COMMENTlink written 3.4 years ago by Christian2.6k
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