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