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Vitalina Komashko (Unlicensed)

Vitalina Komashko (Unlicensed)

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  1. Project proposal
  2. Literature
    1. MINT markers
    2. Shen, 2007 CIMP CpGs on 450k platform
    3. Laird (2006, 2011) markers
  3. Platform
    1. IlluminaHumanMethylation450k.db Bioconductor package
  4. Clinical information
    1. Correlation with technical variables (processing batch/slide)
    2. Clinical variables of interest
  5. DNA methylation
    1. 27k array platform
      1. Normalization
      2. Correlation of processing batch with clinical variables
      3. Shen, 2007: attempt to reproduce results
      4. Laird 2006, 2011 markers: attempt to reproduce results
    2. 450k array platform
      1. Reading raw data files (.idat)
      2. Relationship between various types of batches in the data
      3. Normalization
      4. Shen, 2007: attempt to reproduce the results using TCGA data
  6. more

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