Dahlquist:Edge Software Protocol

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This protocol is for running the Edge software for DNA microarray data anlysis.

Directions for Launching Edge at the Keck Lab

• Login with your Keck lab username to mason (the names of the machines are on the lower-left corner of the login screens).
• Right-click on the green tabula rasa.
• Choose Terminal.
• Type:

cd Desktop/edge_1.1.290
R

• At this point, the R prompt shows up. Type:

source("edge.r")
edge()

• The Edge GUI should now appear.

Analyzing Data with Edge

• Create two tab-delimited text files for "genes" and "covariates".
• Load both into an Edge session.
• Select "Impute Missing Data" from the menu. Calculat Percent Missing Data. The results are:
  • Percent of genes missing data:
  • Percent of arrays missing data:
  • Overall percent of missing data:
• For KNN Parameters, set:
  • Percent of missing values to tolerate in a gene: 100 (so all genes included)
  • Number of nearest neighbors to use (maximum of 15): 15
  • clicked GO to impute missing data.
• Selected "Identify Differentially Expressed Genes"
  • Class variable is:
  • Covariate giving time points is:
  • Covariate corresponding to individuals is:
  • Choose spline type, accepted default of Natural Cubic Spline, dimension 4
  • Number of null iterations, set to 1000
  • Choose a seed for reproducible results, set to 47
  • 1000 permutations looks like it will take about 10 minutes.
  • Save results as: