Dahlquist:Notebook/Nutrigenomics/2010/01/20

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1/20/10

  • The main goals for today-do the between chip normalization and run GenMAPP on the human prostate cancer model

Media:DChip_array_summary.xls

Between Chip Normalization

The steps that were taken in dChip to normalize the samples

Opening the data files

  1. Open dChip
  2. Click on Analysis and Open Group
  3. Clicked OK because the Data location was already saved on dChip
  4. All of the 32 samples were found and and an array summary file was written

Normalizing the data

  1. Click on Analysis and click Normalize and Model...
  2. Needed to find the median probe intensity (brightness)
  3. Went into the excel document dChip_array_summary
  4. Sorted the 32 samples to find the median, median intensity sample
  5. The median sample was 1_12wk_TRAMP with a median intensity of 184
  6. Clicked OK
  7. After each of the samples were normalized and the image was created I clicked on OK to continue normalizing the subsequent samples
  8. Uploaded the completed files to OpenWetWare

GenMAPP on Human PCa Model

  1. Opened GenMAPP 2.1
  2. Checked to make sure that the human gene database was selected (data - gene database)
  3. Clicked on tools in GenMAPP and clicked on MAPPFinder 2.0 and clicked on Calculate New Results
  4. Clicked to Find File and selected the file for prostate cancer Hs_ED_ProstateCancer_20060130.gex
  5. Clicked OK
  6. Clicked on the boxes for Gene Ontology, Calculate P-value, and I chose the color set Hormone vs Primary and saved the file to my folder on my desktop
  7. Selected increased AND decreased under the criteria
  8. Clicked Run MAPPFinder
  9. Going to follow the same procedure for the other 3 color sets, saving them all on the desktop



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