Dinh/Dinh 2014/NOTES/2014-2-25

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Revision as of 01:02, 1 March 2014 by >Dinh (Created page with "= Notes from Senate Exam = * Dr. Bafna's comments & questions: ** Why are intragenic CGIs considered "orphan" although they are part of a gene body? - they might be intronic ...")
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Notes from Senate Exam[edit]

  • Dr. Bafna's comments & questions:
    • Why are intragenic CGIs considered "orphan" although they are part of a gene body? - they might be intronic and might not regulate that gene??
    • Include details on how linkage disequilibrium is calculated on the slides
    • What are the potential offtarget effects of padlock probes, explain how we measured the specificity.
    • We do not know if DNA methylation inherited through the germline, and we should consider that the heritability of DNA methylation might be due to CpG-SNPs
  • Dr. Ren's comments & questions:
    • Use CGIs as control for BSmoothing algorithm & determine the best smoothing window
    • Use Human Epigenome Roadmap project data to find more DMRs
    • Publish TAB-PP paper as a tool for the community.
  • Dr. Zhong's comments & questions:
  • Dr. Chang's comments & questions:
  • Dr. Ideker's comments & questions:
    • Explain the smoothScatter plot --- how are the outliers calculated!!!
    • Check to see if window size for smoothing is affecting segmentation
    • Check to see if low methylation is a signature of the statistics: try CV(unmethyl) and variance (Dr. Zhang suggested)
    • What is the error model for drawing outliers