public static void CalcRatioSignificanceProteinGroups(SilacType type, ICombinedData combinedData, RawFileInfo fileInfo)
{
if (type == SilacType.Doublets)
{
{
List <double> lNormRatio = new List <double>();
List <double> lRatio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lNormRatio.Add(Math.Log(normalizedRatio));
lRatio.Add(Math.Log(ratio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lNormRatio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lNormRatio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA10 = ratioSignificanceA[i];
group.RatioSignificanceB10 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA10(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB10(exp, ratioSignificanceB[i]);
}
}
}
}
if (type == SilacType.Triplets)
{
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA10 = ratioSignificanceA[i];
group.RatioSignificanceB10 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA10(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB10(exp, ratioSignificanceB[i]);
}
}
}
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio20(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA20 = ratioSignificanceA[i];
group.RatioSignificanceB20 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio20(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA20(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB20(exp, ratioSignificanceB[i]);
}
}
}
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio21(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA21 = ratioSignificanceA[i];
group.RatioSignificanceB21 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio21(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA21(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB21(exp, ratioSignificanceB[i]);
}
}
}
}
}
