Dinh/Dinh 2012/NOTES/2012-2-17
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BSPP Data Cleanup[edit]
- The result from simulation is on genome-miner: /home/dinh/Tech_Rep_9/SimulationResults_2172012_header
- Columns:
1 - CpG site 2-10 - Raw data mC|RD 11 - observed STDEV 12 - minimum RD at this site 13 - mean methylation level 14 - average simulated STDEV 15 - p-value from 500 simulations
- There are 184,624 CpGs (out of 412,476) with p-value < 0.05
- of these, 42,329 CpGs have a simulated average STD >= 0.1
- So using a cutoff of p-value < 0.05 and simulated average STD >= 0.1, we will label 42,329 (~10.5%) sites as "bad".