This method filters differentially expressed genes from the Expression Matrix and generates a FeatureSet and filtered Expression Matrix. Begin by selecting or importing both the Expression Matrix and the Genome associated with the Expression Matrix using the Add Data button. If the Expression Matrix was not associated with a Genome when it was imported, please run the method Associate Expression Matrix to Genome Features on the Expression Matrix before running this method. Select either of the filter options that use the Number of Features, or a P-value cutoff to filter differentially expressed genes. If both the Number of Features and the P-value cutoff are populated, the method will default to using the Number of Features with the selected filtering method. Provide names for the output filtered Expression Matrix and FeatureSet and then run the method.

Description of filtering methods to do differential Expression:

• Log odds ratio is a statistical test that calculates the logarithm of the ratio of the odds for regulation to the odds against regulation to measure association between the variables.
• ANOVA (ANalysis Of VAriance) is a statistical test for measurement of heterogeneity of means by analysis of group variances.

Team members who developed & deployed algorithm in KBase: Shinjae Yoo, Paramvir Dehal, Roman Sutormin, Michael Sneddon, Srividya Ramakrishnan, Pavel Novichkov, Keith Keller, Sunita Kumari, Priya Ranjan, Fei He, Jim Thomason, Vivek Kumar.

For questions, e-mail [email protected]