Package ubic.gemma.core.analysis.preprocess.batcheffects
-
Interface Summary Interface Description BatchInfoPopulationHelperService BatchInfoPopulationService Retrieve batch information from the data source, if possible, and populate it into experiments.ExpressionExperimentBatchCorrectionService ExpressionExperimentBatchInformationService Provides status of batch information for datasets.ScanDateExtractor Generic interface for classes that extract scan dates from raw data files. -
Class Summary Class Description AffyScanDateExtractor Extract the scan date from Affymetrix CEL files.AgilentScanDateExtractor Because agilent makes slides that work with any scanner, the formats are not that predictable.BaseScanDateExtractor BatchConfound Represents a summary of a batch effect confound.BatchConfoundUtils Test if an experimental design is confounded with batches.BatchEffectDetails provide some basic information about the properties and strength of a batch effect, if any.BatchInfoParser Parse information on batch from raw data files.BatchInfoPopulationHelperServiceImpl BatchInfoPopulationServiceImpl Retrieve batch information from the data source, if possible, and populate it into experiments.ExpressionExperimentBatchCorrectionServiceImpl Methods for correcting batch effects.ExpressionExperimentBatchInformationServiceImpl GenericScanFileDateExtractor Looks through text file looking for a date near the top of the file in a reasonable format. -
Exception Summary Exception Description BatchInfoMissingException Indicate that batch information is missing.BatchInfoPopulationException Used to indicate a problem with the population of batch information for a givenExpressionExperiment.FASTQHeadersPresentButNotUsableException Indicates that FASTQ headers were present, but were not in a format that yields usable information on batches.SingletonBatchesException Indicates that batches with only a single sample were found, which means we don't form batches at all.UnsupportedRawdataFileFormatException Used to indicate failure was due to the format being unusable, but the files are available.