DiffExTest (Gemma 1.32.2-SNAPSHOT Test API)

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 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

All Methods Instance Methods Concrete Methods
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

- Constructor Detail
  - DiffExTest
```
public DiffExTest()
```
- Method Detail
  - tearDown
```
public void tearDown()
```
  - testCountData
```
public void testCountData()
                   throws Exception
```
    Test differential expression analysis on RNA-seq data. See bug 3383. R code in voomtest.R
    
    Throws:
    
    Exception
  - testGSE35930
```
public void testGSE35930()
                  throws Exception
```
    Test where probes have constant values. See bug 3177.
    
    Throws:
    
    Exception