Package ubic.gemma.core.analysis.expression.diff

Class DiffExTest

java.lang.Object

org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

ubic.gemma.core.util.test.BaseTest

ubic.gemma.core.util.test.BaseIntegrationTest

ubic.gemma.core.util.test.BaseSpringContextTest

ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

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

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class DiffExTest
extends AbstractGeoServiceTest

Tests added to check various cases of differential expression analysis.

Author:

Paul

Field Summary

Fields

Modifier and Type	Field	Description
final NetworkAvailableRule	networkAvailableRule

Fields inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

externalDatabaseService, log, persisterHelper, rule, taxonService, testHelper

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

applicationContext, logger

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 ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest

getTestFileBasePath, getTestFileBasePath

Methods inherited from class ubic.gemma.core.util.test.BaseSpringContextTest

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 ubic.gemma.core.util.test.BaseIntegrationTest

setUpAuthentication, tearDownSecurityContext

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

setApplicationContext

Methods inherited from class java.lang.Object

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

Field Details

networkAvailableRule

public final NetworkAvailableRule networkAvailableRule

Constructor Details

DiffExTest

public DiffExTest()

Method Details

tearDown

public void tearDown()

testCountData

@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

@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