Dahlquist:Notebook/Microarray Data Analysis/2008/10/14: Difference between revisions
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(Autocreate 2008/10/14 Entry for Dahlquist:Notebook/Microarray_Data_Analysis) |
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== Today's Workflow == | == Today's Workflow == | ||
* First compared dCIN5 and wt data following the same procedure as outlined on 10/02/2008: | |||
** 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. | |||
* Results: (Saved in 2008-10-14 Results) | |||
** No significant genes under these settings. | |||
** Choose Q-Value cutoff as 1, recalculate | |||
** Saved total list of genes as: "20081014_wt_dCIN5_comparison_results_allgenes" in "Data analysis 2008-10-02" | |||
** Saved | |||
Revision as of 12:18, 14 October 2008
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Today's Workflow
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