public void CompareAveragingWithMSstats()
{
var srmDocument = LoadRatPlasmaDocument();
var documentContainer = new MemoryDocumentContainer();
documentContainer.SetDocument(documentContainer.Document, srmDocument);
GroupComparisonModel model = new GroupComparisonModel(documentContainer, null);
model.GroupComparisonDef = GroupComparisonDef.EMPTY.ChangeControlAnnotation("Condition")
.ChangeControlValue("Healthy")
.ChangeIdentityAnnotation("BioReplicate")
.ChangeSummarizationMethod(SummarizationMethod.AVERAGING)
.ChangePerProtein(false);
var expectedValues = MsStatsTestUtil.ReadExpectedResults(typeof(MSstatsAveragingTest),
"RatPlasmaTestingResult.csv");
var groupComparer = new GroupComparer(model.GroupComparisonDef, srmDocument, new QrFactorizationCache());
foreach (var protein in srmDocument.PeptideGroups)
{
foreach (var peptide in protein.Peptides)
{
var result = groupComparer.CalculateFoldChange(new GroupComparisonSelector(protein, peptide, IsotopeLabelType.light, null, new GroupIdentifier("Diseased")), null);
var expectedResult = expectedValues[peptide.Peptide.Sequence];
Assert.AreEqual(expectedResult.EstimatedValue, result.LinearFitResult.EstimatedValue,
(expectedResult.StandardError + result.LinearFitResult.StandardError) * 2, peptide.Peptide.Sequence);
}
}
}
public void TestFoldChangeWithNoNormalization()
{
SrmDocument testDocument = OpenTestDocument();
var expectedResults = MsStatsTestUtil.ReadExpectedResults(typeof(MsStatsNormalizationTest),
"BrudererSubsetNoNormalization_TestingResult.csv");
GroupComparisonDef groupComparisonDef = new GroupComparisonDef("test")
.ChangeControlValue("S2")
.ChangeCaseValue("S1")
.ChangeControlAnnotation("Condition")
.ChangeIdentityAnnotation("BioReplicate")
.ChangePerProtein(true)
.ChangeNormalizationMethod(NormalizationMethod.NONE);
VerifyFoldChanges(testDocument, groupComparisonDef, expectedResults);
}
public void RunTestFoldChangeEqualizeMedians(bool asSmallMolecules)
{
SrmDocument testDocument = OpenTestDocument();
if (testDocument == null)
{
Assume.IsTrue(asSmallMolecules);
return;
}
var expectedResults = MsStatsTestUtil.ReadExpectedResults(typeof(MsStatsNormalizationTest),
"BrudererSubsetEqualizeMedians_TestingResult.csv");
GroupComparisonDef groupComparisonDef = new GroupComparisonDef("test")
.ChangeControlValue("S2")
.ChangeCaseValue("S1")
.ChangeControlAnnotation("Condition")
.ChangeIdentityAnnotation("BioReplicate")
.ChangePerProtein(true)
.ChangeNormalizationMethod(NormalizationMethod.EQUALIZE_MEDIANS);
VerifyFoldChanges(testDocument, groupComparisonDef, expectedResults);
}