public void TestBenjaminiHochbergFdrCorrectionAgainstRWithNaNs()
{
var pValues = new[]
{
double.NaN,
0.55418364, 0.33169014, 0.61117003, 0.79263279, 0.74714936,
0.93567141, 0.41151512, 0.99690655, 0.57863046, 0.35048756, double.NaN,
0.17302064, 0.58728787, 0.45285588, 0.67122903, 0.99010006,
0.32346151, 0.02248119, 0.5575581, 0.54179022, 0.30518608
};
var expectedFdrs = new[]
{
double.NaN,
0.87310004, 0.87310004, 0.87310004, 0.93250916, 0.93250916,
0.99690655, 0.87310004, 0.99690655, 0.87310004, 0.87310004, double.NaN,
0.87310004, 0.87310004, 0.87310004, 0.89497204, 0.99690655,
0.87310004, 0.4496238, 0.87310004, 0.87310004, 0.87310004
};
PerseusPluginUtils.CalcBenjaminiHochbergFdr(pValues, 0.05, out var fdrs);
for (int i = 0; i < expectedFdrs.Length; i++)
{
var expected = expectedFdrs[i];
var actual = fdrs[i];
if (double.IsNaN(expected) && double.IsNaN(actual))
{
continue;
}
Assert.AreEqual(expected, actual, 0.00001);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] cols = param.GetParam <int[]>("Columns").Value;
int truncIndex = param.GetParam <int>("Use for truncation").Value;
TestTruncation truncation = truncIndex == 0
? TestTruncation.Pvalue
: (truncIndex == 1 ? TestTruncation.BenjaminiHochberg : TestTruncation.PermutationBased);
double threshold = param.GetParam <double>("Threshold value").Value;
int sideInd = param.GetParam <int>("Side").Value;
TestSide side;
switch (sideInd)
{
case 0:
side = TestSide.Both;
break;
case 1:
side = TestSide.Left;
break;
case 2:
side = TestSide.Right;
break;
default:
throw new Exception("Never get here.");
}
foreach (int col in cols)
{
BaseVector r = mdata.Values.GetColumn(col);
double[] pvals = CalcSignificanceA(r, side);
string[][] fdr;
switch (truncation)
{
case TestTruncation.Pvalue:
fdr = PerseusPluginUtils.CalcPvalueSignificance(pvals, threshold);
break;
case TestTruncation.BenjaminiHochberg:
double[] fdrs;
fdr = PerseusPluginUtils.CalcBenjaminiHochbergFdr(pvals, threshold, pvals.Length, out fdrs);
break;
default:
throw new Exception("Never get here.");
}
mdata.AddNumericColumn(mdata.ColumnNames[col] + " Significance A", "", pvals);
mdata.AddCategoryColumn(mdata.ColumnNames[col] + " A significant", "", fdr);
}
}
public void TestBenjaminiHochberFdrCorrectionKinactExample()
{
var pValues = new[]
{
0.5, 0.26996402, 0.17923912, 0.29354353, double.NaN
};
var expectedFdrs = new[]
{
0.5, 0.39139137, 0.39139137, 0.39139137, double.NaN
};
PerseusPluginUtils.CalcBenjaminiHochbergFdr(pValues, 0.05, out var fdrs);
for (int i = 0; i < expectedFdrs.Length; i++)
{
Assert.AreEqual(expectedFdrs[i], fdrs[i], 0.00001);
}
}
public void TestBenjaminiHochbergFdrCorrectionWithSinglePvalue()
{
var pValues = new[]
{
0.55418364,
};
var expectedFdrs = new[]
{
0.55418364,
};
PerseusPluginUtils.CalcBenjaminiHochbergFdr(pValues, 0.05, out var fdrs);
for (int i = 0; i < expectedFdrs.Length; i++)
{
Assert.AreEqual(expectedFdrs[i], fdrs[i], 0.00001);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] rcols = param.GetParam <int[]>("Ratio columns").Value;
int[] icols = param.GetParam <int[]>("Intensity columns").Value;
if (rcols.Length == 0)
{
processInfo.ErrString = "Please specify some ratio columns.";
return;
}
if (rcols.Length != icols.Length)
{
processInfo.ErrString = "The number of ratio and intensity columns have to be equal.";
return;
}
int truncIndex = param.GetParam <int>("Use for truncation").Value;
TestTruncation truncation = truncIndex == 0
? TestTruncation.Pvalue
: (truncIndex == 1 ? TestTruncation.BenjaminiHochberg : TestTruncation.PermutationBased);
double threshold = param.GetParam <double>("Threshold value").Value;
int sideInd = param.GetParam <int>("Side").Value;
TestSide side;
switch (sideInd)
{
case 0:
side = TestSide.Both;
break;
case 1:
side = TestSide.Left;
break;
case 2:
side = TestSide.Right;
break;
default:
throw new Exception("Never get here.");
}
for (int i = 0; i < rcols.Length; i++)
{
BaseVector r = mdata.Values.GetColumn(rcols[i]);
BaseVector intens = icols[i] < mdata.ColumnCount
? mdata.Values.GetColumn(icols[i])
: new DoubleArrayVector(mdata.NumericColumns[icols[i] - mdata.ColumnCount]);
double[] pvals = CalcSignificanceB(r, intens, side);
string[][] fdr;
switch (truncation)
{
case TestTruncation.Pvalue:
fdr = PerseusPluginUtils.CalcPvalueSignificance(pvals, threshold);
break;
case TestTruncation.BenjaminiHochberg:
fdr = PerseusPluginUtils.CalcBenjaminiHochbergFdr(pvals, threshold, out double[] fdrs);
break;
default:
throw new Exception("Never get here.");
}
mdata.AddNumericColumn(mdata.ColumnNames[rcols[i]] + " Significance B", "", pvals);
mdata.AddCategoryColumn(mdata.ColumnNames[rcols[i]] + " B significant", "", fdr);
}
}
public void TestBenjaminiHochbergFdrCorrectionWithoutValues()
{
PerseusPluginUtils.CalcBenjaminiHochbergFdr(new double[0], 0.05, out var fdrs);
Assert.AreEqual(0, fdrs.Length);
}
