Class BatchInfoPopulationServiceImpl
- java.lang.Object
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- ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationServiceImpl
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- All Implemented Interfaces:
BatchInfoPopulationService
@Service public class BatchInfoPopulationServiceImpl extends Object implements BatchInfoPopulationService
Retrieve batch information from the data source, if possible, and populate it into experiments.- Author:
- paul
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Constructor Summary
Constructors Constructor Description BatchInfoPopulationServiceImpl()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
fillBatchInformation(ExpressionExperiment ee, boolean force)
Attempt to obtain batch information from the data provider and populate it into the given experiment.static boolean
isBatchFactor(ExperimentalFactor ef)
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Method Detail
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isBatchFactor
public static boolean isBatchFactor(ExperimentalFactor ef)
- Parameters:
ef
- ef- Returns:
- true if the factor seems to be a 'batch' factor.
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fillBatchInformation
@Transactional public void fillBatchInformation(ExpressionExperiment ee, boolean force) throws BatchInfoPopulationException
Description copied from interface:BatchInfoPopulationService
Attempt to obtain batch information from the data provider and populate it into the given experiment. The method used may vary. For GEO, the default method is to download the raw data files, and look in them for a date. This is not implemented for every possible type of raw data file. For RNA-seq, we look for FASTQ headers under the configured FASTQ_HEADERS_ROOT.- Specified by:
fillBatchInformation
in interfaceBatchInfoPopulationService
- Parameters:
ee
- the experimentforce
- whether to force recomputation- Throws:
BatchInfoPopulationException
- describing the issue with populating batch information
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