public void TestMedianPolishExamples()
{
var matrix = new double?[, ]
{
{
1677120562, 1057244128, 1573838418, 1610727572, 1700424094, 1337004885, 2096688822, 556694100,
1758444441
},
{ 822328116, 698575767, 557625726, 1867460568, 1497452757, 1286780009, 2109397777, 63595003, 579931872 },
{ 2021080567, 1939792651, 998333669, 309807657, 766650568, 1525104204, 98432661, 1273392816, 423985426 },
{ 310985865, 1892567676, 834287094, 1778432993, 99139496, 2020064656, 1859647279, 1208352316, 673041733 }
};
var expectedResult = new MedianPolish()
{
OverallConstant = 1250365665,
RowEffects = new double[]
{ 367804634, -369087286, -130763091, 130763091 },
ColumnEffects = new double[] { 0, 164368154, -222460779, 194930755, -135349106, 405501630, 478518523, -495229908, -498481827 },
Residuals = new double?[, ]
{
{ 58950263, -725294325, 178128898, -202373482, 217602900, -686667045, 0, -566246291, 638755969 },
{ -58950263, -347070766, -101191874, 791251435, 751523484, 0, 749600876, -322453468, 197135321 },
{ 901477993, 655821923, 101191874, -1004725672, -217602900, 0, -1499688436, 649020150, -197135321 },
{ -1070142891, 347070766, -324380884, 202373482, -1146640155, 233434270, 0, 322453468, -209605196 }
}
};
MedianPolish medianPolish = MedianPolish.GetMedianPolish(matrix, 0.01, 10);
Assert.AreEqual(expectedResult.OverallConstant, medianPolish.OverallConstant);
AssertDoublesEqual(expectedResult.RowEffects, medianPolish.RowEffects);
AssertDoublesEqual(expectedResult.ColumnEffects, medianPolish.ColumnEffects);
AssertMatricesEqual(expectedResult.Residuals, medianPolish.Residuals);
}
public void TestMedianPolishSimpleMissingValues()
{
var matrix = new double?[, ] {
{ null, 1, 2 }, { 3, 4, 5 }, { 6, null, 7 }
};
MedianPolish medianPolish = MedianPolish.GetMedianPolish(matrix, 0, 100);
Assert.AreEqual(4, medianPolish.OverallConstant);
AssertDoublesEqual(new[] { -3.000000, 0.000000, 2.333333 }, medianPolish.RowEffects, .0001);
AssertDoublesEqual(new[] { -6.666667e-01, -6.223015e-61, 1.000000e+00 }, medianPolish.ColumnEffects, .0001);
}
public void TestMedianPolishSimpleMatrix()
{
var matrix = new double?[, ] {
{ 1, 3 }, { 2, 5 }
};
MedianPolish medianPolish = MedianPolish.GetMedianPolish(matrix, 0.01, 10);
Assert.AreEqual(2.75, medianPolish.OverallConstant);
CollectionAssert.AreEqual(new[] { -.75, .75 }, medianPolish.RowEffects);
CollectionAssert.AreEqual(new[] { -1.25, 1.25 }, medianPolish.ColumnEffects);
}
public void TestMedianPolishMissingValues()
{
/* matrix(c(NA, 1057244128, 1573838418, 1610727572, 1700424094, 1337004885, 2096688822, 556694100,1758444441,
* 822328116, NA, 557625726, 1867460568, 1497452757, 1286780009, 2109397777,63595003, 579931872,
* 2021080567, 1939792651, 998333669, 309807657, 766650568, 1525104204, 98432661, 1273392816, 423985426,
* 310985865, 1892567676, 834287094, 1778432993, 99139496, 2020064656, 1859647279, 1208352316, 673041733),nrow = 4, byrow = TRUE) */
var matrix = new double?[, ]
{
{ null, 1057244128, 1573838418, 1610727572, 1700424094, 1337004885, 2096688822, 556694100, 1758444441 },
{ 822328116, null, 557625726, 1867460568, 1497452757, 1286780009, 2109397777, 63595003, 579931872 },
{ 2021080567, 1939792651, 998333669, 309807657, 766650568, 1525104204, 98432661, 1273392816, 423985426 },
{ 310985865, 1892567676, 834287094, 1778432993, 99139496, 2020064656, 1859647279, 1208352316, 673041733 }
};
var expectedResult =
new MedianPolish()
{
OverallConstant = 1162563201,
RowEffects = new double[] { 119681337, -129549460, 16173465, -16173465 },
ColumnEffects =
new double[]
{
-210685625, 746177940, -246252819, 480263146, 3046729, 300066903, 763850914, -331793929,
-463214936
},
Residuals = new double?[, ]
{
{
null, -971178350, 537846699, -151780112, 415132827, -245306556, 50593371, -393756509, 939414839
},
{ 0, null, -229135195, 354183682, 461392287, -46300635, 312533123, -637624809, 10133067 },
{
1053029526, 14878045, 65849823, -1349192154, -415132827, 46300635, -1844154918, 426450079,
-291536304
},
{ -624718246, 0, -65849823, 151780112, -1050296969, 573608017, -50593371, 393756509, -10133067 }
}
};
MedianPolish medianPolish = MedianPolish.GetMedianPolish(matrix, 0.01, 10);
Assert.AreEqual(expectedResult.OverallConstant, medianPolish.OverallConstant, 1);
AssertDoublesEqual(expectedResult.RowEffects, medianPolish.RowEffects);
AssertDoublesEqual(expectedResult.ColumnEffects, medianPolish.ColumnEffects);
AssertMatricesEqual(expectedResult.Residuals, medianPolish.Residuals);
}
private IList <RunAbundance> SummarizeDataRowsWithMedianPolish(IList <DataRowDetails> dataRows)
{
IList <IGrouping <IdentityPath, DataRowDetails> > dataRowsByFeature =
SumMs1Transitions(dataRows).ToLookup(row => row.IdentityPath)
.Where(IncludeFeatureForMedianPolish)
.ToArray();
#pragma warning disable 162
// ReSharper disable HeuristicUnreachableCode
if (false)
{
// For debugging purposes, we might want to order these features in the same order as MSstats R code
Array.Sort((IGrouping <IdentityPath, DataRowDetails>[])dataRowsByFeature, (group1, group2) =>
{
String s1 = GetFeatureKey(SrmDocument, group1.Key);
String s2 = GetFeatureKey(SrmDocument, group2.Key);
return(String.Compare(s1.ToLowerInvariant(), s2.ToLowerInvariant(), StringComparison.Ordinal));
});
}
// ReSharper restore HeuristicUnreachableCode
#pragma warning restore 162
var featureCount = dataRowsByFeature.Count;
if (featureCount == 0)
{
return(ImmutableList.Empty <RunAbundance>());
}
var rows = new List <double?[]>();
IDictionary <int, int> replicateRowIndexes = new Dictionary <int, int>();
for (int iFeature = 0; iFeature < dataRowsByFeature.Count; iFeature++)
{
foreach (DataRowDetails dataRowDetails in dataRowsByFeature[iFeature])
{
int rowIndex;
if (!replicateRowIndexes.TryGetValue(dataRowDetails.ReplicateIndex, out rowIndex))
{
rowIndex = rows.Count;
rows.Add(new double?[featureCount]);
replicateRowIndexes.Add(dataRowDetails.ReplicateIndex, rowIndex);
}
var row = rows[rowIndex];
row[iFeature] = dataRowDetails.GetLog2Abundance();
}
}
var matrix = new double?[rows.Count, featureCount];
for (int iRow = 0; iRow < rows.Count; iRow++)
{
for (int iCol = 0; iCol < featureCount; iCol++)
{
matrix[iRow, iCol] = rows[iRow][iCol];
}
}
var medianPolish = MedianPolish.GetMedianPolish(matrix);
List <RunAbundance> runAbundances = new List <RunAbundance>();
foreach (var replicateIndexDetails in _replicateIndexes)
{
int rowIndex;
if (!replicateRowIndexes.TryGetValue(replicateIndexDetails.Key, out rowIndex))
{
continue;
}
double value = medianPolish.OverallConstant + medianPolish.RowEffects[rowIndex];
runAbundances.Add(new RunAbundance()
{
ReplicateIndex = replicateIndexDetails.Key,
BioReplicate = replicateIndexDetails.Value.BioReplicate,
Control = replicateIndexDetails.Value.IsControl,
Log2Abundance = value
});
}
return(runAbundances);
}
