//attempt to normalize a numaric column
public void Normalize(int col, NormalizationMethod method = NormalizationMethod.StandardScore)
{
//https://docs.microsoft.com/en-us/azure/machine-learning/studio-module-reference/normalize-data
//https://en.wikipedia.org/wiki/Normalization_(statistics)
//https://en.wikipedia.org/wiki/Feature_scaling
switch (method)
{
case NormalizationMethod.StandardScore:
PreformStandardScoreNormalization(col);
break;
case NormalizationMethod.FeatureScalingStandardization:
PreformStandardization(col);
break;
case NormalizationMethod.FeatureScalingMinMax:
PreformMinMaxNormalization(col);
break;
case NormalizationMethod.FeatureScalingMean:
PreformMeanNormalization(col);
break;
default:
throw new Exception("How did you even get here? Please let the monkey that" +
"coded this know the following: \"MatrixData<T>.Normalize.default\", along with" +
"what you did to cause this error");
}
}
protected override object[] GetDropdownItems()
{
var document = SkylineDataSchema.Document;
List <Tuple <string, NormalizationMethod> > normalizationMethods
= new List <Tuple <string, NormalizationMethod> >
{
new Tuple <string, NormalizationMethod>(string.Empty, null)
};
normalizationMethods.AddRange(NormalizationMethod.ListNormalizationMethods(document).Select(ToDropdownItem));
normalizationMethods.AddRange(NormalizationMethod.RatioToSurrogate.ListSurrogateNormalizationMethods(document).Select(ToDropdownItem));
// If there are any molecules that have a normalization method that is not in the list, add it to the end.
var normalizationMethodValues = new HashSet <NormalizationMethod>(normalizationMethods.Select(tuple => tuple.Item2)
.Where(normalizationMethod => null != normalizationMethod));
foreach (var molecule in document.Molecules)
{
if (molecule.NormalizationMethod != null &&
normalizationMethodValues.Add(molecule.NormalizationMethod))
{
normalizationMethods.Add(ToDropdownItem(molecule.NormalizationMethod));
}
}
return(normalizationMethods.Cast <object>().ToArray());
}
/// <summary>
/// Construct a ResNodeHiden data for build a ResNet
/// </summary>
/// <param name="size">hidden size</param>
/// <param name="normalization">Which normalizatoin to use</param>
/// <param name="dropoutRate">dropout rate</param>
public ResNodeDenseDef(int size, NormalizationMethod normalization, float dropoutRate = 0)
{
HiddenSize = size;
NormalizationMethod = normalization;
DropoutRate = dropoutRate;
ParameterNames = new List <string>();
}
private IList <Tuple <string, NormalizationMethod> > GetDropdownItems(SrmDocument document)
{
List <Tuple <string, NormalizationMethod> > normalizationMethods
= new List <Tuple <string, NormalizationMethod> >
{
new Tuple <string, NormalizationMethod>(string.Empty, null)
};
if (null != document)
{
normalizationMethods.AddRange(NormalizationMethod.ListNormalizationMethods(document).Select(ToDropdownItem));
normalizationMethods.AddRange(NormalizationMethod.RatioToSurrogate.ListSurrogateNormalizationMethods(document).Select(ToDropdownItem));
// If there are any molecules that have a normalization method that is not in the list, add it to the end.
var normalizationMethodValues = new HashSet <NormalizationMethod>(normalizationMethods.Select(tuple => tuple.Item2)
.Where(normalizationMethod => null != normalizationMethod));
foreach (var molecule in document.Molecules)
{
if (molecule.NormalizationMethod != null &&
normalizationMethodValues.Add(molecule.NormalizationMethod))
{
normalizationMethods.Add(ToDropdownItem(molecule.NormalizationMethod));
}
}
}
return(normalizationMethods);
}
protected override void UpdateSettings()
{
var groupComparisonDef = GroupComparisonModel.GroupComparisonDef;
ReplaceComboItems(comboControlAnnotation, ListReplicateAnnotations(), groupComparisonDef.ControlAnnotation);
string[] controlValues = ListControlValues();
ReplaceComboItems(comboControlValue, controlValues, groupComparisonDef.ControlValue ?? string.Empty);
var caseValues = new HashSet <string>(controlValues)
{
string.Empty
};
if (null != groupComparisonDef.ControlValue)
{
caseValues.Remove(groupComparisonDef.ControlValue);
}
var sortedCaseValues = caseValues.ToArray();
Array.Sort(sortedCaseValues);
ReplaceComboItems(comboCaseValue, sortedCaseValues, groupComparisonDef.CaseValue ?? string.Empty);
ReplaceComboItems(comboIdentityAnnotation, new[] { string.Empty }.Concat(ListReplicateAnnotations()),
groupComparisonDef.IdentityAnnotation);
ReplaceComboItems(comboNormalizationMethod, NormalizationMethod.ListNormalizationMethods(GroupComparisonModel.Document, true), groupComparisonDef.NormalizationMethod);
tbxConfidenceLevel.Text = groupComparisonDef.ConfidenceLevelTimes100.ToString(CultureInfo.CurrentCulture);
radioScopeProtein.Checked = groupComparisonDef.PerProtein;
radioScopePeptide.Checked = !groupComparisonDef.PerProtein;
}
/// <summary>
/// Construct a dense layer data for build
/// </summary>
/// <param name="size">hidden size</param>
/// <param name="normalization">Which normalizatoin to use</param>
/// <param name="dropoutRate">dropout rate</param>
public LayerDenseDef(int size, NormalizationMethod normalization, LayerDef activationDef, float dropoutRate = 0)
{
HiddenSize = size;
NormalizationMethod = normalization;
DropoutRate = dropoutRate;
ParameterNames = new List <string>();
Activation = activationDef;
}
public double?GetTransitionValue(NormalizationMethod normalizationMethod, PeptideDocNode peptideDocNode, TransitionGroupDocNode transitionGroupDocNode, TransitionDocNode transitionDocNode, TransitionChromInfo transitionChromInfo)
{
if (!transitionDocNode.IsQuantitative(Document.Settings))
{
return(null);
}
if (transitionChromInfo == null || transitionChromInfo.IsEmpty)
{
return(null);
}
if (TryGetDenominator(normalizationMethod, transitionGroupDocNode.LabelType, transitionChromInfo.FileId,
out double?denominator))
{
return(transitionChromInfo.Area / denominator);
}
if (normalizationMethod is NormalizationMethod.RatioToLabel ratioToLabel)
{
if (ratioToLabel.IsotopeLabelTypeName == transitionGroupDocNode.LabelType.Name)
{
return(null);
}
if (SimpleRatios)
{
return(null);
}
var otherTransitionGroup =
FindMatchingTransitionGroup(ratioToLabel, peptideDocNode, transitionGroupDocNode);
if (otherTransitionGroup == null)
{
return(null);
}
var otherTransition = FindMatchingTransition(transitionGroupDocNode, transitionDocNode, otherTransitionGroup);
if (otherTransition == null)
{
return(null);
}
if (!otherTransition.IsQuantitative(Document.Settings))
{
return(null);
}
var otherChrominfo = FindMatchingTransitionChromInfo(transitionChromInfo, otherTransition);
if (otherChrominfo == null || otherChrominfo.IsEmpty)
{
return(null);
}
return(transitionChromInfo.Area / otherChrominfo.Area);
}
return(null);
}
public void NormalizeAll(NormalizationMethod method = NormalizationMethod.StandardScore, bool ignoreDT = false)
{
for (int col = 0; col < NumberOfColumns; col++)
{
if (IsValueNumaric(col) | ignoreDT)
{
Normalize(col, method);
}
}
}
public override int GetHashCode()
{
unchecked
{
var hashCode = RegressionWeighting.GetHashCode();
hashCode = (hashCode * 397) ^ RegressionFit.GetHashCode();
hashCode = (hashCode * 397) ^ NormalizationMethod.GetHashCode();
hashCode = (hashCode * 397) ^ MsLevel.GetHashCode();
hashCode = (hashCode * 397) ^ (Units == null ? 0 : Units.GetHashCode());
return(hashCode);
}
}
public static NormalizeOption FromPersistedName(string name)
{
if (string.IsNullOrEmpty(name))
{
return(FromNormalizationMethod(NormalizationMethod.NONE));
}
if (_specialOptions.TryGetValue(name, out Special specialNormalizeOption))
{
return(specialNormalizeOption);
}
return(FromNormalizationMethod(NormalizationMethod.FromName(name)));
}
void IXmlSerializable.ReadXml(XmlReader reader)
{
RegressionWeighting = RegressionWeighting.Parse(reader.GetAttribute(Attr.weighting));
RegressionFit = RegressionFit.Parse(reader.GetAttribute(Attr.fit));
NormalizationMethod = NormalizationMethod.FromName(reader.GetAttribute(Attr.normalization));
MsLevel = reader.GetNullableIntAttribute(Attr.ms_level);
Units = reader.GetAttribute(Attr.units);
bool empty = reader.IsEmptyElement;
reader.Read();
if (!empty)
{
reader.ReadEndElement();
}
}
public double?GetTransitionValue(NormalizationMethod normalizationMethod, PeptideDocNode peptideDocNode,
TransitionDocNode transitionDocNode, TransitionChromInfo transitionChromInfo)
{
if (peptideDocNode == null)
{
return(null);
}
var transitionGroupDocNode = (TransitionGroupDocNode)peptideDocNode.FindNode(transitionDocNode.Transition.Group);
if (transitionGroupDocNode == null)
{
return(null);
}
return(GetTransitionValue(normalizationMethod, peptideDocNode, transitionGroupDocNode, transitionDocNode,
transitionChromInfo));
}
public override int GetHashCode()
{
unchecked
{
var hashCode = RegressionWeighting.GetHashCode();
hashCode = (hashCode * 397) ^ RegressionFit.GetHashCode();
hashCode = (hashCode * 397) ^ NormalizationMethod.GetHashCode();
hashCode = (hashCode * 397) ^ MsLevel.GetHashCode();
hashCode = (hashCode * 397) ^ (Units == null ? 0 : Units.GetHashCode());
hashCode = (hashCode * 397) ^ LodCalculation.GetHashCode();
hashCode = (hashCode * 397) ^ MaxLoqBias.GetHashCode();
hashCode = (hashCode * 397) ^ MaxLoqCv.GetHashCode();
hashCode = (hashCode * 397) ^ SimpleRatios.GetHashCode();
return(hashCode);
}
}
private object ParseValue(string value, Type type)
{
if (string.IsNullOrEmpty(value))
{
return(null);
}
if (type == typeof(SampleType))
{
return(SampleType.FromName(value));
}
if (type == typeof(NormalizationMethod))
{
return(NormalizationMethod.FromName(value));
}
return(Convert.ChangeType(value, type, DataSchema.DataSchemaLocalizer.FormatProvider));
}
/// <summary>
/// Returns the normalization options that are appropriate for the document.
/// Note: never includes "Default", "None", "Total", or "Maximum".
/// </summary>
/// <param name="document"></param>
/// <returns></returns>
public static IEnumerable <NormalizeOption> AvailableNormalizeOptions(SrmDocument document)
{
foreach (var normalizationMethod in NormalizationMethod.ListNormalizationMethods(document)
.OrderBy(method => method is NormalizationMethod.RatioToLabel ? 0 : 1))
{
if (Equals(normalizationMethod, NormalizationMethod.NONE))
{
continue;
}
yield return(FromNormalizationMethod(normalizationMethod));
}
if (document.Settings.PeptideSettings.Quantification.RegressionFit != RegressionFit.NONE)
{
yield return(CALIBRATED);
}
}
void IXmlSerializable.ReadXml(XmlReader reader)
{
RegressionWeighting = RegressionWeighting.Parse(reader.GetAttribute(Attr.weighting));
RegressionFit = RegressionFit.Parse(reader.GetAttribute(Attr.fit));
NormalizationMethod = NormalizationMethod.FromName(reader.GetAttribute(Attr.normalization));
MsLevel = reader.GetNullableIntAttribute(Attr.ms_level);
Units = reader.GetAttribute(Attr.units);
LodCalculation = LodCalculation.Parse(reader.GetAttribute(Attr.lod_calculation));
MaxLoqBias = reader.GetNullableDoubleAttribute(Attr.max_loq_bias);
MaxLoqCv = reader.GetNullableDoubleAttribute(Attr.max_loq_cv);
bool empty = reader.IsEmptyElement;
reader.Read();
if (!empty)
{
reader.ReadEndElement();
}
}
public static string NormalizeTag(string tag, NormalizationMethod method)
{
string output = string.Empty;
if (!string.IsNullOrEmpty(tag))
{
output = tag.Trim().TrimStart('#').Trim();
switch (method)
{
case NormalizationMethod.NonSpaced: output = NormalizeNonSpaced(output); break;
case NormalizationMethod.Spaced: output = NormalizeSpaced(output); break;
default: throw new NotImplementedException();
}
}
return("#" + output);
}
public bool TryGetDenominator(NormalizationMethod normalizationMethod, IsotopeLabelType labelType, ChromFileInfoId fileId, out double?denominator)
{
if (Equals(normalizationMethod, NormalizationMethod.NONE))
{
denominator = 1;
return(true);
}
FileInfo fileInfo;
if (!_fileInfos.TryGetValue(fileId, out fileInfo))
{
denominator = null;
return(true);
}
if (Equals(normalizationMethod, NormalizationMethod.GLOBAL_STANDARDS))
{
denominator = fileInfo.GlobalStandardArea;
return(true);
}
if (Equals(normalizationMethod, NormalizationMethod.EQUALIZE_MEDIANS))
{
var normalizationData = _normalizationData.Value;
var medianAdjustment = normalizationData.GetMedian(fileId, labelType) - normalizationData.GetMedianMedian(fileInfo.SampleType, labelType);
if (!medianAdjustment.HasValue)
{
denominator = null;
return(true);
}
denominator = 1 / Math.Pow(2, medianAdjustment.Value);
return(true);
}
if (normalizationMethod is NormalizationMethod.RatioToSurrogate ratioToSurrogate)
{
denominator = fileInfo.GetSurrogateStandardArea(ratioToSurrogate);
return(true);
}
denominator = null;
return(false);
}
public void TestDilutionFactor()
{
var baseDocument = LoadTestDocument();
baseDocument = ChangeQuantificationSettings(baseDocument,
QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeRegressionFit(RegressionFit.LINEAR)
.ChangeUnits("ng/mL"));
var baseCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(baseDocument.Settings,
baseDocument.MoleculeGroups.First(), baseDocument.Molecules.First());
var baseCurve = baseCurveFitter.GetCalibrationCurve();
// Set the dilution factor of each external standard to 2.0, and each unknown to 3.0
var docWithDilutionFactor = baseDocument.ChangeMeasuredResults(
baseDocument.MeasuredResults.ChangeChromatograms(baseDocument.MeasuredResults.Chromatograms.Select(
chrom => Equals(chrom.SampleType, SampleType.STANDARD) ? chrom.ChangeDilutionFactor(2.0) :
chrom.ChangeDilutionFactor(3.0)).ToArray()));
var dilutionFactorCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(
docWithDilutionFactor.Settings, docWithDilutionFactor.MoleculeGroups.First(),
docWithDilutionFactor.Molecules.First());
var dilutionFactorCurve = dilutionFactorCurveFitter.GetCalibrationCurve();
Assert.AreEqual(2.0 * baseCurve.Slope, dilutionFactorCurve.Slope);
Assert.AreEqual(baseCurve.Intercept, dilutionFactorCurve.Intercept);
for (int replicateIndex = 0; replicateIndex < baseDocument.MeasuredResults.Chromatograms.Count; replicateIndex++)
{
var sampleType = baseDocument.MeasuredResults.Chromatograms[replicateIndex].SampleType;
var baseConcentration = baseCurveFitter.GetCalculatedConcentration(baseCurve, replicateIndex);
Assert.IsNotNull(baseConcentration);
var dilutionFactorConcentration =
dilutionFactorCurveFitter.GetCalculatedConcentration(dilutionFactorCurve, replicateIndex);
Assert.IsNotNull(dilutionFactorConcentration);
if (Equals(sampleType, SampleType.STANDARD))
{
Assert.AreEqual(baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
else
{
Assert.AreEqual(1.5 * baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
}
AssertEx.ValidatesAgainstSchema(docWithDilutionFactor);
}
public void TestSinglePointExternalCalibrationWithIsConcentration()
{
const double internalStandardConcentration = 80.0;
var srmDocument = LoadTestDocument();
srmDocument = ChangeStandardConcentrationCount(srmDocument, 1);
srmDocument = ChangeQuantificationSettings(srmDocument, QuantificationSettings.DEFAULT
.ChangeRegressionFit(RegressionFit.LINEAR_THROUGH_ZERO)
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy)));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = protein.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(internalStandardConcentration);
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(srmDocument.Settings, protein, peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, srmDocument.Settings);
Assert.AreEqual(CalibrationCurveFitter.ConcentrationRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy),
curveFitter.GetXAxisTitle());
Assert.AreEqual(CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy), curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = peptide.Results[iReplicate].First().LabelRatios.First().Ratio.Ratio;
double?actualY = curveFitter.GetYValue(iReplicate).Value;
Assert.IsNotNull(actualY);
Assert.AreEqual(expectedY, actualY.Value, epsilon, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.AreEqual(1, calibrationCurve.PointCount);
var expectedConcentration = expectedY * internalStandardConcentration / calibrationCurve.Slope.Value;
Assert.AreEqual(expectedConcentration / internalStandardConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
var chromatogramSet = chromatograms[iReplicate];
if (Equals(chromatogramSet.SampleType, SampleType.STANDARD) && chromatogramSet.AnalyteConcentration.HasValue)
{
// Since there was only one standard, the regression line goes exactly through this sample.
Assert.AreEqual(expectedConcentration, chromatogramSet.AnalyteConcentration.Value * peptide.ConcentrationMultiplier.GetValueOrDefault(1.0), epsilon);
}
}
}
protected void UpdateSettings()
{
var groupComparisonDef = GroupComparisonModel.GroupComparisonDef;
ReplaceComboItems(comboControlAnnotation, ListReplicateAnnotations(), groupComparisonDef.ControlAnnotation);
string[] controlValues = ListControlValues();
ReplaceComboItems(comboControlValue, controlValues, groupComparisonDef.ControlValue ?? string.Empty);
var caseValues = new HashSet <string>(controlValues)
{
string.Empty
};
if (null != groupComparisonDef.ControlValue)
{
caseValues.Remove(groupComparisonDef.ControlValue);
}
var sortedCaseValues = caseValues.ToArray();
Array.Sort(sortedCaseValues);
ReplaceComboItems(comboCaseValue, sortedCaseValues, groupComparisonDef.CaseValue ?? string.Empty);
ReplaceComboItems(comboIdentityAnnotation, new[] { string.Empty }.Concat(ListReplicateAnnotations()),
groupComparisonDef.IdentityAnnotation);
ReplaceComboItems(comboNormalizationMethod, NormalizationMethod.ListNormalizationMethods(GroupComparisonModel.Document), groupComparisonDef.NormalizationMethod);
ReplaceComboItems(comboSummaryMethod, SummarizationMethod.ListSummarizationMethods(), groupComparisonDef.SummarizationMethod);
tbxConfidenceLevel.Text = groupComparisonDef.ConfidenceLevelTimes100.ToString(CultureInfo.CurrentCulture);
radioScopeProtein.Checked = groupComparisonDef.PerProtein;
radioScopePeptide.Checked = !groupComparisonDef.PerProtein;
cbxUseZeroForMissingPeaks.Checked = groupComparisonDef.UseZeroForMissingPeaks;
cbxUseZeroForMissingPeaks.Visible = GroupComparisonModel.Document.Settings.PeptideSettings.Integration.PeakScoringModel != null;
if (GroupComparisonDef.QValueCutoff.HasValue)
{
tbxQValueCutoff.Text = groupComparisonDef.QValueCutoff.Value.ToString(CultureInfo.CurrentCulture);
groupBoxQValueCutoff.Visible = true;
}
else
{
tbxQValueCutoff.Text = string.Empty;
}
if (RequiresAdvanced(groupComparisonDef))
{
ShowAdvanced(true);
}
}
public static IEnumerable <QuantificationSettings> ListAllQuantificationSettings()
{
foreach (var normalizationMethod in
new[] { NormalizationMethod.NONE, NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy), })
{
foreach (var regressionFit in RegressionFit.All)
{
foreach (var weighting in RegressionWeighting.All)
{
foreach (var msLevel in new int?[] { 1, 2, null })
{
yield return(new QuantificationSettings(weighting)
.ChangeNormalizationMethod(normalizationMethod)
.ChangeRegressionFit(regressionFit)
.ChangeMsLevel(msLevel));
}
}
}
}
}
public double?GetTransitionGroupValue(NormalizationMethod normalizationMethod, PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionGroupChromInfo transitionGroupChromInfo)
{
if (transitionGroupChromInfo == null)
{
return(null);
}
if (TryGetDenominator(normalizationMethod, transitionGroupDocNode.LabelType,
transitionGroupChromInfo.FileId, out double?denominator))
{
return(transitionGroupChromInfo.Area / denominator);
}
if (normalizationMethod is NormalizationMethod.RatioToLabel ratioToLabel)
{
return(GetTransitionGroupRatioValue(ratioToLabel, peptideDocNode, transitionGroupDocNode, transitionGroupChromInfo)?.Ratio);
}
return(null);
}
public void TestInternalCalibration()
{
const double internalStandardConcentration = 80.0;
var srmDocument = LoadTestDocument();
AssertEx.IsDocumentState(srmDocument, null, 1, 1, 2, 10);
srmDocument = ChangeStandardConcentrationCount(srmDocument, 0);
srmDocument = ChangeQuantificationSettings(srmDocument,
QuantificationSettings.DEFAULT
.ChangeRegressionFit(RegressionFit.NONE)
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeUnits("ng/mL"));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = protein.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(internalStandardConcentration);
CalibrationCurveFitter curveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(srmDocument.Settings, protein, peptide);
string expectedXAxis = CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, "ng/mL");
Assert.AreEqual(expectedXAxis, curveFitter.GetXAxisTitle());
string expectedYAxis = CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy);
Assert.AreEqual(expectedYAxis, curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = peptide.Results[iReplicate].First().LabelRatios.First().Ratio.Ratio;
Assert.AreEqual(expectedY, curveFitter.GetYValue(iReplicate).Value, epsilon, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.AreEqual(1 / internalStandardConcentration, calibrationCurve.Slope);
Assert.IsNull(calibrationCurve.RSquared);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
}
}
public static ResNodeDenseDef[] ResNodeLayers(int numOfNodes, int hiddenSize, NormalizationMethod normalizatoin = NormalizationMethod.None, float dropout = 0.0f)
{
var result = new ResNodeDenseDef[numOfNodes];
for (int i = 0; i < numOfNodes; ++i)
{
result[i] = new ResNodeDenseDef(hiddenSize, normalizatoin, dropout);
}
return(result);
}
public static LayerDenseDef[] DenseLayers(int numOfLayers, int hiddenSize, bool hasBias = true, NormalizationMethod normalizatoin = NormalizationMethod.None, float dropout = 0.0f, float initialWeightScale = 0.1f, LayerDef activation = null)
{
var result = new LayerDenseDef[numOfLayers];
for (int i = 0; i < numOfLayers; ++i)
{
result[i] = new LayerDenseDef(hiddenSize, normalizatoin, activation, dropout);
result[i].HasBias = hasBias;
result[i].InitialWeightScale = initialWeightScale;
}
return(result);
}
public QuantificationSettings ChangeNormalizationMethod(NormalizationMethod normalizationMethod)
{
return(ChangeProp(ImClone(this), im => im.NormalizationMethod = normalizationMethod));
}
protected override void DoTest()
{
Settings.Default.CalibrationCurveOptions.DisplaySampleTypes = new[]
{ SampleType.UNKNOWN.Name, SampleType.QC.Name, SampleType.STANDARD.Name };
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
Assert.AreEqual(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available,
calibrationForm.ZedGraphControl.GraphPane.Title.Text);
PauseForScreenShot("Blank document");
RunUI(() =>
{
SkylineWindow.OpenFile(TestFilesDir.GetTestPath("CalibrationTest.sky"));
});
Assert.AreEqual(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve,
GetGraphTitle(calibrationForm));
PauseForScreenShot("No peptide selected");
RunUI(() => SkylineWindow.SequenceTree.SelectedPath = SkylineWindow.DocumentUI.GetPathTo(
(int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
Assert.AreEqual(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_,
GetGraphTitle(calibrationForm));
PauseForScreenShot("Quantification not configured");
{
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUi.QuantNormalizationMethod = NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = "ng/mL";
});
PauseForScreenShot("Peptide Settings - Quantification tab");
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
}
PauseForScreenShot("Normalization without Internal Standard Concentration");
WaitForOpenForm <CalibrationForm>();
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
var documentGrid = FindOpenForm <DocumentGridForm>();
// Now, specify an internal standard concentration.
RunUI(() => documentGrid.ChooseView("PeptidesWithCalibration"));
WaitForConditionUI(() => documentGrid.IsComplete);
RunUI(() =>
{
var colInternalStandardQuantification =
documentGrid.FindColumn(PropertyPath.Root.Property("InternalStandardConcentration"));
documentGrid.DataGridView.Rows[0].Cells[colInternalStandardQuantification.Index].Value = 80.0;
SkylineWindow.ShowCalibrationForm();
});
Assert.IsNull(GetGraphTitle(calibrationForm));
PauseForScreenShot("Internal calibration only");
RunUI(() =>
{
var colInternalStandardQuantification =
documentGrid.FindColumn(PropertyPath.Root.Property("InternalStandardConcentration"));
documentGrid.DataGridView.Rows[0].Cells[colInternalStandardQuantification.Index].Value = null;
});
FillInSampleTypesAndConcentrations();
WaitForGraphs();
{
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUi.QuantNormalizationMethod = NormalizationMethod.NONE;
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
});
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
RunUI(() => SkylineWindow.ShowCalibrationForm());
}
PauseForScreenShot("External Calibration Without Internal Standard");
{
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.QuantNormalizationMethod = NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy));
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
}
PauseForScreenShot("External Calibration normalized to heavy");
RunUI(() => documentGrid.ChooseView("PeptidesWithCalibration"));
WaitForConditionUI(() => documentGrid.IsComplete);
RunUI(() =>
{
var colInternalStandardQuantification =
documentGrid.FindColumn(PropertyPath.Root.Property("InternalStandardConcentration"));
documentGrid.DataGridView.Rows[0].Cells[colInternalStandardQuantification.Index].Value = 80.0;
SkylineWindow.ShowCalibrationForm();
});
PauseForScreenShot("External calibration with internal standard concentration specified");
TestAllQuantificationSettings();
}
public static NormalizeOption FromNormalizationMethod(NormalizationMethod normalizationMethod)
{
return(new Simple(normalizationMethod));
}
public bool Is(NormalizationMethod normalizationMethod)
{
return(Equals(NormalizationMethod, normalizationMethod));
}