Uses of Class
ubic.gemma.core.analysis.preprocess.PreprocessingException

Packages that use PreprocessingException

Package	Description
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.loader.expression	This package contains interfaces and classes for loading expression data.

Uses of PreprocessingException in ubic.gemma.core.analysis.preprocess

Subclasses of PreprocessingException in ubic.gemma.core.analysis.preprocess

Modifier and Type	Class	Description
class	FilteringRelatedPreprocessingException
class	QuantitationTypeConversionRelatedPreprocessingException
class	QuantitationTypeDetectionRelatedPreprocessingException	An exception that wraps a QuantitationTypeDetectionException.
class	SampleCoexpressionRelatedPreprocessingException	Exception raised in preprocessing when there is a problem with sample coexpression analysis.
class	SVDRelatedPreprocessingException	Exception raised if a SVD cannot be computed.

Methods in ubic.gemma.core.analysis.preprocess that throw PreprocessingException

Modifier and Type	Method	Description
Integer	PreprocessorHelperService.batchCorrect(ExpressionExperiment ee)	If possible, batch-correct the processed data vectors via ComBat.
Integer	PreprocessorHelperServiceImpl.batchCorrect(ExpressionExperiment ee)	If possible, batch correct the processed data vectors.
default void	PreprocessorService.process(ExpressionExperiment ee)	Preprocess a dataset.
default void	PreprocessorService.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)	Preprocess a dataset.
void	PreprocessorService.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticFailure)	Preprocess a dataset.
void	PreprocessorServiceImpl.process(ExpressionExperiment ee, boolean ignoreQuantitationMismatch, boolean ignoreDiagnosticsFailure)
void	PreprocessorService.processDiagnostics(ExpressionExperiment ee)	Create or update the sample correlation, PCA and M-V data.
void	PreprocessorServiceImpl.processDiagnostics(ExpressionExperiment ee)
void	PreprocessorHelperService.processForMeanVarianceRelation(ExpressionExperiment ee)	Compute and persist the mean-variance scatter used for the heteroscedasticity diagnostic plot.
void	PreprocessorHelperServiceImpl.processForMeanVarianceRelation(ExpressionExperiment ee)	Create the scatter plot to evaluate heteroscedasticity.

Uses of PreprocessingException in ubic.gemma.core.analysis.preprocess.batcheffects

Subclasses of PreprocessingException in ubic.gemma.core.analysis.preprocess.batcheffects

Modifier and Type	Class	Description
class	BatchInfoMissingException	Indicate that batch information is missing.
class	BatchInfoPopulationException	Used to indicate a problem with the population of batch information for a given ExpressionExperiment.
class	FASTQHeadersPresentButNotUsableException	Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.
class	SingletonBatchesException	Indicates that batches with only a single sample were found, which means we don't form batches at all.
class	UnsupportedRawdataFileFormatException	Used to indicate failure was due to the format being unusable, but the files are available.

Uses of PreprocessingException in ubic.gemma.core.loader.expression

Subclasses of PreprocessingException in ubic.gemma.core.loader.expression

Modifier and Type	Class	Description
class	RawDataPostprocessingException	Raised by DataUpdater when new raw data was stored for an experiment, but post-processing it failed.