Package ubic.gemma.core.analysis.expression.diff
package ubic.gemma.core.analysis.expression.diff
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ClassDescriptionException raised when all analyses fail.Exception raised when all subset analyses failed with an
AnalysisException.Base exception for all differential analysis-related exceptions.Defines the different types of analyses our linear modeling framework supports: GENERICLM - generic linear regression (interactions are omitted, but this could change) OSTTEST - one sample t-test OWA - one-way ANOVA TTEST - two sample t-test TWO_WAY_ANOVA_WITH_INTERACTION TWO_WAY_ANOVA_NO_INTERACTIONUtilities for deciding if a factor value is a baseline condition.Holds the settings used for differential expression analysis, and defines some defaults.Service methods to do database-related work for differential expression analysisTransactional methods for dealing with differential expression analyses.A helper class for the differential expression analyzers.Differential expression service to run the differential expression analysis (and persist the results using the appropriate data access objects).A value object with meta analysis results.Used to perform meta-analyses of complete data sets (actually result sets), select the top genes, and potentially store the results.A command object with a selected factor and associated experiment.Occurs when empirical bayes estimation fails.Provides access toDifferentialExpressionAnalysisResults and meta-analysis results.* @author francesException raised when a log2 conversion fails.Handles fitting linear models with continuous or fixed-level covariates.Exception raised when suitable factor is left for analysis.Exception raised when no sample is left for analysis.