Dahlquist:Notebook/Microarray Data Analysis/2008/10/02

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Microarray Data Analysis
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Kevin's Edge Analysis from 10/2/2008
cd Desktop/edge_1.1.290 R source("edge.r") edge
 * 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:
 * At this point, the R prompt shows up. Type:
 * The Edge GUI should now appear.
 * Create two tab-delimited text files for "genes" and "covariates".
 * Files in Desktop "Data analysis 2008-10-02"
 * Used gene file "wt-dCIN5_consolidated_Edge_genes-indexonly_20080715.txt"
 * Used covariate file "wt-dCIN5_consolidated_Edge_covariates_20080710.txt
 * Load both into an Edge session.
 * Select "Impute Missing Data" from the menu. Calculate Percent Missing Data by clicking on the button.  The results are:
 * Percent of genes missing data: 7.63%
 * Percent of arrays missing data: 95.35%
 * Overall percent of missing data: 3.15%
 * 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"
 * Note: this is to compare between the wt and dCIN5 strains. Different parameters and gene/covariate files will need to be used to analyze individual strains.
 * Class Variable is: Strain
 * Differential Expression Type is: Time Course
 * Number of null iterations, set to 1000
 * Choose a seed for reproducible results, set to 47
 * Choose Time Course Settings
 * Covariate giving time points is: Timepoint
 * Covariate corresponding to individuals is: Flask
 * Choose spline type, accepted default of Natural Cubic Spline, dimension 4
 * Click "Apply" and then click "Go"
 * 1000 permutations looks like it will take about 10 minutes.
 * Save results as:
 * Choose Q-Value cutoff as 1, recalculate
 * Saved total list of genes as: "20081002_wt_dCIN5_comparison_results_genelist" in "Data analysis 2008-10-02"
 * Can cluster significant genes, did not do


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