Dahlquist:Notebook/Nutrigenomics/2010/02/24

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2/24/10

GenMAPP Day 2

  • Created color sets for the four primary comparisons in my study
  1. WT12 vs. WT24
  2. WT12 vs. TRAMPwater24
  3. WT12 vs. TRAMPtreatTumorFree24
  4. WT12 vs. TRAMPtreatTumors24
  • The following criterion was set in GenMAPP
    For increased-LogFC>0.25 and P-value <0.05
    For decreased-LogFC<-0.25 and P-value <0.05
  • Colors were set-increased Red and decreased Green
  • Once the color sets were set I proceeded on to the MAPPFinder program

MAPPFinder

  • From GenMAPP I accessed MAPPFinder and followed the protocol from the bioinformatics lab for each of the four color sets that I ran


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