Class ProcessedExpressionDataVectorCreationHelperServiceTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorCreationHelperServiceTest

public class ProcessedExpressionDataVectorCreationHelperServiceTest
extends BaseIntegrationTest5

Constructor Summary

Constructors

Constructor	Description
ProcessedExpressionDataVectorCreationHelperServiceTest()

Method Summary

Modifier and Type	Method	Description
void	testCreateProcessedDataVectors()
void	testCreateProcessedDataVectorsFromLog2Data()
void	testCreateProcessedDataVectorsFromLog2RatiometricData()
void	testCreateProcessedDataVectorsWithARowMissingInEverySample()	A row with no value in any sample survives quantile normalization untouched.
void	testReadProcessedDataInputsInitializesDesignElementSequences()	The sample-correlation matrix is built from what readProcessedDataInputs returns, with no transaction open, and AffyProbeNameFilter then reads each design element's sequence name.
void	testThaw()

Methods inherited from class BaseIntegrationTest5

setUpAuthentication, tearDownSecurityContext

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ProcessedExpressionDataVectorCreationHelperServiceTest

public ProcessedExpressionDataVectorCreationHelperServiceTest()

Method Details

testCreateProcessedDataVectors

@Test
public void testCreateProcessedDataVectors()
                                    throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

testCreateProcessedDataVectorsFromLog2Data

@Test
public void testCreateProcessedDataVectorsFromLog2Data()
                                                throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

testCreateProcessedDataVectorsFromLog2RatiometricData

@Test
public void testCreateProcessedDataVectorsFromLog2RatiometricData()
                                                           throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

testCreateProcessedDataVectorsWithARowMissingInEverySample

@Test
public void testCreateProcessedDataVectorsWithARowMissingInEverySample()
                                                                throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

A row with no value in any sample survives quantile normalization untouched. The normalizer drops such rows before it ranks, so its output has fewer rows than its input; writing the result back by the input's row count ran off the end. frinkbro hit it on GSE21509 (eid 30208, 2026-09-14) through corrMat -force: Index 45708 out of bounds for length 45708 against 46,628 design elements.

4,000 rows is the smallest size that is normalized at all.

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

testReadProcessedDataInputsInitializesDesignElementSequences

@Test
public void testReadProcessedDataInputsInitializesDesignElementSequences()
                                                                  throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

The sample-correlation matrix is built from what readProcessedDataInputs returns, with no transaction open, and AffyProbeNameFilter then reads each design element's sequence name. The sequences must leave the read initialized: GSE96826 (ee 15112) failed with a LazyInitializationException on a BioSequence proxy at exactly that point.

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

testThaw

@Test
public void testThaw()
              throws QuantitationTypeDetectionException,
QuantitationTypeConversionException

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException