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".