How to aggregate multiple copy number variation profiles or select the best one for one sample
1
1
Entering edit mode
7.3 years ago
fbrundu ▴ 310

Hi,

I downloaded copy-number-variation data from the TCGA portal. However, I found that for some samples could be present multiple replicates. Supposing I want a single copy number variation profile for each sample, how can I select the best one or aggregate the replicates?

Thanks

copy-number-variation tcga RNA-Seq • 2.2k views
ADD COMMENT
2
Entering edit mode
7.3 years ago
  • Considering samples from the same patient 'replicates' is potentially dangerous. Spatial heterogeneity in solid tumors may mean that two samples have very different profiles.
  • If the primary difference is just multiple platforms from the same tumor subsection, you can probably just use the highest-resolution method and call it a day.
  • If you want to get complicated, you can look at this method out of Terry Speed's lab, but my feeling is that it's probably more hassle than it's worth, in general. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660872/
ADD COMMENT

Login before adding your answer.

Traffic: 2260 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6