Class DiffExTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest5

ubic.gemma.core.analysis.expression.diff.DiffExTest

@Tag("slow")
@ExtendWith(NetworkAvailableExtension.class)
public class DiffExTest
extends AbstractGeoServiceTest5

Tests added to check various cases of differential expression analysis.

Author:

Paul

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
DiffExTest()

Method Summary

Modifier and Type	Method	Description
void	tearDown()
void	testCountData()	Test differential expression analysis on RNA-seq data.
void	testGSE35930()	Test where probes have constant values.

Methods inherited from class AbstractGeoServiceTest5

getTestFileBasePath, getTestFileBasePath

Methods inherited from class BaseSpringContextTest5

addTestAnalyses, countRowsInTable, deleteFromTables, getJdbcTemplate, getNewTestPersistentCompleteExpressionExperiment, getTaxon, getTestNonPersistentBioSequence, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentBasicExpressionExperiment, getTestPersistentBasicExpressionExperiment, getTestPersistentBibliographicReference, getTestPersistentBioAssay, getTestPersistentBioAssay, getTestPersistentBioMaterial, getTestPersistentBioMaterial, getTestPersistentBioSequence, getTestPersistentBioSequence, getTestPersistentBioSequence2GeneProducts, getTestPersistentBlatResult, getTestPersistentBlatResult, getTestPersistentCompleteExpressionExperiment, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentContact, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentExpressionExperiment, getTestPersistentExpressionExperiment, getTestPersistentGene, getTestPersistentGene, getTestPersistentGeneProduct, getTestPersistentQuantitationType, randomName, resetTestCollectionSize, runAsAdmin, runAsAgent, runAsAnonymous, runAsUser, runAsUser, setTestCollectionSize

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

DiffExTest

public DiffExTest()

Method Details

tearDown

@AfterEach
public void tearDown()

testCountData

@Test
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testCountData()
                   throws Exception

Test differential expression analysis on RNA-seq data. See bug 3383. R code in voomtest.R

Throws:

Exception

testGSE35930

@Test
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testGSE35930()
                  throws Exception

Test where probes have constant values. See bug 3177.

Throws:

Exception