Feature: Add Relative Standard Error to Calibration Metrics

pwiz_tools/Skyline/Controls/Graphs/Calibration/CalibrationGraphControl.cs

@@ -78,7 +78,7 @@ protected override void OnHandleCreated(EventArgs e)
 
         private void Settings_OnPropertyChanged(object sender, PropertyChangedEventArgs e)
         {
-            if (e.PropertyName == nameof(Properties.Settings.Default.CalibrationCurveOptions ))
+            if (e.PropertyName == nameof(Properties.Settings.Default.CalibrationCurveOptions))
             {
                 Update(DisplaySettings);
             }
@@ -355,6 +355,11 @@ private void DoUpdate(Settings displaySettings)
                     labelLines.Add(CalibrationCurveMetrics.RSquaredDisplayText(CalibrationCurveMetrics.RSquared.Value));
                 }
 
+                if (CalibrationCurveMetrics.RelativeStandardError.HasValue)
+                {
+                    labelLines.Add(CalibrationCurveMetrics.RelativeStandardErrorDisplayText(CalibrationCurveMetrics.RelativeStandardError.Value));
+                }
+
                 if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
                 {
                     labelLines.Add(string.Format(@"{0}: {1}",
@@ -406,7 +411,7 @@ private void DoUpdate(Settings displaySettings)
                         {
                             ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Raw, xSelected.Value,
                                     ySelected.Raw)
-                                { Line = { Color = GraphSummary.ColorSelected } };
+                            { Line = { Color = GraphSummary.ColorSelected } };
                             zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
                             var verticalLine = new LineObj(xSelected.Value, ySelected.Raw, xSelected.Value,
                                 options.LogYAxis ? minY / 10 : 0)
@@ -439,7 +444,7 @@ private void DoUpdate(Settings displaySettings)
                                 // If the point has a specified concentration, then use that.
                                 ArrowObj arrow = new ArrowObj(xSpecified.Value, ySelected.Raw, xSpecified.Value,
                                         ySelected.Raw)
-                                    { Line = { Color = GraphSummary.ColorSelected } };
+                                { Line = { Color = GraphSummary.ColorSelected } };
                                 zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
                             }
                             else
@@ -726,7 +731,7 @@ ToolStripMenuItem excludeStandardMenuItem
                 menuStrip.Items.Insert(index++, moreDisplayOptionsContextMenuItem);
                 menuStrip.Items.Insert(index++, new ToolStripSeparator());
             }
-            
+
         }
         private bool IsEnableIsotopologResponseCurve()
         {

pwiz_tools/Skyline/Model/Databinding/Entities/CalibrationCurveMetrics.cs

@@ -75,6 +75,21 @@ public CalibrationCurveMetrics ChangeRSquared(double? rSquared)
             return ChangeProp(ImClone(this), im => im.RSquared = rSquared);
         }
 
+        [Format(Formats.Integer, NullValue = TextUtil.EXCEL_NA)]
+        public int? FittedParameters { get; private set; }
+        public CalibrationCurveMetrics ChangeFittedParameters(int? fittedParameters)
+        {
+            return ChangeProp(ImClone(this), im => im.FittedParameters = fittedParameters);
+        }
+
+        [Format(Formats.Percent, NullValue = TextUtil.EXCEL_NA)]
+        public double? RelativeStandardError { get; private set; }
+
+        public CalibrationCurveMetrics ChangeRelativeStandardError(double? relStdError)
+        {
+            return ChangeProp(ImClone(this), im => im.RelativeStandardError = relStdError);
+        }
+
         public string ErrorMessage { get; private set; }
         public CalibrationCurveMetrics ChangeErrorMessage(string errorMessage)
         {
@@ -136,5 +151,11 @@ public static string RSquaredDisplayText(double rSquared)
             return QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
                    rSquared.ToString(@"0.####");
         }
+
+        public static string RelativeStandardErrorDisplayText(double relStdError)
+        {
+            return QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_RelativeStandardError +
+                   relStdError.ToString(@"0.##%");
+        }
     }
 }

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.ja.resx

@@ -507,6 +507,9 @@
   <data name="FirstPosition">
     <value>最初の位置</value>
   </data>
+  <data name="FittedParameters">
+    <value>推定パラメータ</value>
+  </data>
   <data name="FoldChange">
     <value>倍率変化</value>
   </data>
@@ -1428,6 +1431,9 @@
   <data name="RSquared">
     <value>R平方</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>相対標準誤差</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>試料希釈倍数</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.resx

@@ -507,6 +507,9 @@
   <data name="FirstPosition">
     <value>First Position</value>
   </data>
+  <data name="FittedParameters">
+    <value>Fitted Parameters</value>
+  </data>
   <data name="FoldChange">
     <value>Fold Change</value>
   </data>
@@ -1431,6 +1434,9 @@
   <data name="RSquared">
     <value>R Squared</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>Relative Standard Error</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>Sample Dilution Factor</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.zh-CHS.resx

@@ -507,6 +507,9 @@
   <data name="FirstPosition">
     <value>第一个位置</value>
   </data>
+  <data name="FittedParameters">
+    <value>拟合参数</value>
+  </data>
   <data name="FoldChange">
     <value>倍数变化</value>
   </data>
@@ -1428,6 +1431,9 @@
   <data name="RSquared">
     <value>R 平方</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>相对标准误差</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>样品稀释因子</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnToolTips.ja.resx

@@ -495,6 +495,9 @@
   <data name="FirstPosition">
     <value>ペプチドに含まれるタンパク質シークエンスの最初の（N末端）アミノ酸の位置です。タンパク質シークエンスがない場合には#N/Aとなります。</value>
   </data>
+  <data name="FittedParameters">
+    <value>検量線において、校正データに適合されたパラメータ（例：傾き、切片）の数。</value>
+  </data>
   <data name="FoldChange">
     <value>倍率変化値。倍率変化とは、対照群の正規化強度に対する治療群の正規化強度の比率です。</value>
   </data>
@@ -1451,6 +1454,9 @@
   <data name="RSquared">
     <value>決定係数</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>相対標準誤差</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>試料が分析される前に希釈される量です。
 外部標準の希釈倍率は一般的に1で、不明の試料は、装置の定量可能範囲に収まるようにするため1を上回る倍率で希釈された可能性があります。</value>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnToolTips.resx

@@ -514,6 +514,9 @@ to be the Analyte Concentration from the Replicate times the Concentration Multi
     <value>The position of the first (N-terminal) amino acid of the peptide within its
 containing protein sequence, or #N/A if no protein sequence is available.</value>
   </data>
+  <data name="FittedParameters">
+    <value>The number of parameters fitted to calibration data in the calibration curve.</value>
+  </data>
   <data name="FoldChange">
     <value>The fold change value. The fold change is the ratio of the normalized intensity of the treatment group to the normalized intensity of the control group.</value>
   </data>
@@ -1547,6 +1550,9 @@ retention score calculator, if one is used (e.g. SSRCalc or iRT score)
   <data name="RSquared">
     <value>Coefficient of determination</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>Relative Standard Error</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>The amount by which the sample was diluted before being analyzed. 
 External standards typically have a dilution factor of 1, and unknown samples may have been diluted by a factor greater than 1 in order to bring them into the quantifiable range for the instrument.</value>

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnToolTips.zh-CHS.resx

@@ -514,6 +514,9 @@
     <value>肽段的第一个 (N-末端) 氨基酸在其包含的蛋白质序列中的位置，
 如果没有可用的蛋白质序列，则为 #N/A。</value>
   </data>
+  <data name="FittedParameters">
+    <value>校准曲线中拟合至校准数据的参数（例如斜率、截距）数量</value>
+  </data>
   <data name="FoldChange">
     <value>倍数变化值。倍数变化是试验组的归一化强度与对照组归一化强度的比率。</value>
   </data>
@@ -1530,6 +1533,9 @@
   <data name="RSquared">
     <value>测定系数</value>
   </data>
+  <data name="RelativeStandardError">
+    <value>相对标准误差</value>
+  </data>
   <data name="SampleDilutionFactor">
     <value>在分析之前稀释样品的量。
 外部标准通常具有 1 的稀释因子，并且未知样品可能已被稀释大于 1 的因子，以使它们进入仪器的可量化范围。</value>

pwiz_tools/Skyline/Model/DocSettings/AbsoluteQuantification/CalibrationCurve.cs

@@ -32,7 +32,7 @@ public static readonly CalibrationCurve NO_EXTERNAL_STANDARDS
 
         public double? GetY(double? x)
         {
-            return x == null ? (double?) null : GetY(x.Value);
+            return x == null ? (double?)null : GetY(x.Value);
         }
         public abstract double GetY(double x);
 
@@ -61,13 +61,54 @@ public CalibrationCurveMetrics GetMetrics(IList<WeightedPoint> points)
                 {
                     calibrationCurveRow = calibrationCurveRow.ChangeRSquared(rSquared);
                 }
+                // Assuming the fields are already populated as needed
+                double? relStdError = CalculateRelativeStandardError(points, calibrationCurveRow.FittedParameters);
+                if (relStdError.HasValue)
+                {
+                    calibrationCurveRow = calibrationCurveRow.ChangeRelativeStandardError(relStdError);
+                }
             }
             return calibrationCurveRow;
         }
 
         protected abstract CalibrationCurveMetrics CreateCalibrationCurveMetrics();
         public abstract override string ToString();
 
+        /// <summary>
+        /// Returns Relative Standard Error (formatted typically as a percent like %RSD).
+        /// This method uses degrees of freedom (n - p) which depends on the calibration type
+        /// and which parameters are allowed to be fitted (e.g., intercept forced through 0 or not).
+        /// </summary>
+        public virtual double? CalculateRelativeStandardError(IList<WeightedPoint> points, int? fittedParameters)
+        {
+            if (!fittedParameters.HasValue) 
+            {
+                return null;
+            }
+            List<double> relativeErrors = new List<double>();
+            foreach (var point in points)
+            {
+                double? xFitted = GetX(point.Y);
+                if (xFitted.HasValue && point.X != 0 && !double.IsNaN(xFitted.Value)) 
+                {
+                    relativeErrors.Add((xFitted.Value - point.X) / point.X);
+                }
+
+            }
+            if (!relativeErrors.Any())
+            {
+                return null;
+            }
+            int degreesOfFreedom = relativeErrors.Count - fittedParameters.Value;
+            if (degreesOfFreedom <= 0) 
+            {
+                return null;
+            }
+            double sumOfSquaresOfResiduals = relativeErrors.Sum(r => r * r);
+            double relStdError = Math.Sqrt(sumOfSquaresOfResiduals / degreesOfFreedom);
+            return relStdError;
+        }
+
         public virtual double? CalculateRSquared(IEnumerable<WeightedPoint> points)
         {
             List<double> yValues = new List<double>();
@@ -111,7 +152,11 @@ public override double GetY(double x)
 
             protected override CalibrationCurveMetrics CreateCalibrationCurveMetrics()
             {
-                return new CalibrationCurveMetrics().ChangeSlope(Slope).ChangeIntercept(Intercept);
+
+                return new CalibrationCurveMetrics()
+                    .ChangeSlope(Slope)
+                    .ChangeIntercept(Intercept)
+                    .ChangeFittedParameters(1 + (Intercept.HasValue ? 1 : 0));
             }
 
             public override string ToString()
@@ -164,8 +209,11 @@ public override double GetY(double x)
 
             protected override CalibrationCurveMetrics CreateCalibrationCurveMetrics()
             {
-                return new CalibrationCurveMetrics().ChangeIntercept(Intercept).ChangeSlope(Slope)
-                    .ChangeQuadraticCoefficient(QuadraticCoefficient);
+                return new CalibrationCurveMetrics()
+                    .ChangeIntercept(Intercept)
+                    .ChangeSlope(Slope)
+                    .ChangeQuadraticCoefficient(QuadraticCoefficient)
+                    .ChangeFittedParameters(3); // 2 if intercept forced to 0
             }
 
             public override string ToString()
@@ -213,7 +261,10 @@ public override double GetY(double x)
 
             protected override CalibrationCurveMetrics CreateCalibrationCurveMetrics()
             {
-                return new CalibrationCurveMetrics().ChangeSlope(Slope).ChangeIntercept(Intercept);
+                return new CalibrationCurveMetrics()
+                    .ChangeSlope(Slope)
+                    .ChangeIntercept(Intercept)
+                    .ChangeFittedParameters(2); // 1 if intercept forced to 0
             }
 
             /// <summary>
@@ -288,8 +339,11 @@ public override double GetY(double x)
 
             protected override CalibrationCurveMetrics CreateCalibrationCurveMetrics()
             {
-                return new CalibrationCurveMetrics().ChangeSlope(Slope).ChangeIntercept(Intercept)
-                    .ChangeTurningPoint(TurningPoint);
+                return new CalibrationCurveMetrics()
+                    .ChangeSlope(Slope)
+                    .ChangeIntercept(Intercept)
+                    .ChangeTurningPoint(TurningPoint)
+                    .ChangeFittedParameters(3); // Bilinear turning point counts as fitted parameter
             }
 
             public override string ToString()
@@ -323,7 +377,10 @@ public override double GetY(double x)
 
             protected override CalibrationCurveMetrics CreateCalibrationCurveMetrics()
             {
-                return new CalibrationCurveMetrics().ChangeSlope(Slope).ChangePointCount(0);
+                return new CalibrationCurveMetrics()
+                    .ChangeSlope(Slope)
+                    .ChangePointCount(0)
+                    .ChangeFittedParameters(1); // slope only
             }
 
             public override string ToString()

pwiz_tools/Skyline/Model/DocSettings/AbsoluteQuantification/QuantificationStrings.ja.resx

@@ -358,4 +358,7 @@
     <value>{0} ({1})</value>
     <comment>Example: Standard (MyMolecule)</comment>
   </data>
+  <data name="CalibrationForm_DisplayCalibrationCurve_RelativeStandardError" xml:space="preserve">
+    <value>RSE = </value>
+  </data>
 </root>

pwiz_tools/Skyline/Model/DocSettings/AbsoluteQuantification/QuantificationStrings.resx

@@ -358,4 +358,7 @@
     <value>{0} ({1})</value>
     <comment>Example: Standard (MyMolecule)</comment>
   </data>
+  <data name="CalibrationForm_DisplayCalibrationCurve_RelativeStandardError" xml:space="preserve">
+    <value>RSE = </value>
+  </data>
 </root>

pwiz_tools/Skyline/Model/DocSettings/AbsoluteQuantification/QuantificationStrings.zh-CHS.resx

@@ -358,4 +358,7 @@
     <value>{0} ({1})</value>
     <comment>Example: Standard (MyMolecule)</comment>
   </data>
+  <data name="CalibrationForm_DisplayCalibrationCurve_RelativeStandardError" xml:space="preserve">
+    <value>RSE = </value>
+  </data>
 </root>

pwiz_tools/Skyline/Model/Hibernate/Formats.cs

@@ -42,7 +42,7 @@ public static class Formats
         public const string OneOverK0 = "0.####";
         public const string Percent = "0%";
         public const string PEAK_SCORE = "0.####";
-
+        public const string Integer = "0";
         public const string IonMobility = "0.###";
         public const string CCS = "0.##";
         public const string Skewness = "0.###";