Package ubic.gemma.core.analysis.expression.diff
@NonNullApi
package ubic.gemma.core.analysis.expression.diff
- Author:
- paul, poirigui
-
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.Filter used for performing DEA.Holds the result of data filtering for differential expression analysis.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.Co-bean facade for theDifferentialExpressionAnalysisEventaudit emission carried out at the end ofDifferentialExpressionAnalyzerServiceImpl.persistAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig).Implementation ofDifferentialExpressionAnalyzerAuditService.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.Periodic warm-up of the DEA "find results by gene" path.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.Exception raised when data filtering 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 whenMeanVarianceEstimatorfails.Raised when a factor carries more than one explicitly marked baseline and the analysis was not configured with a subset factor.Exception raised when suitable factor is left for analysis.