Dahlquist:Edge Software Protocol
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This protocol is for running the Edge software for DNA microarray data anlysis.
- Click here to see the Edge manual.
- Click here to link to the Dahlquist Lab Notebook for Microarray Data Analysis.
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: