public static InternalStandard GetClosestInternalStandard(QuantPoint qPt, List <InternalStandard> internalStandards)
{
if (internalStandards.Count == 0)
{
return(null);
}
if (internalStandards.Count == 1)
{
return(internalStandards.First());
}
if (internalStandards.Count > 1)
{
double timeDiff = double.MaxValue;
InternalStandard holdStandard = null;
foreach (var standard in internalStandards)
{
var currDiff = Math.Abs(standard.ApexRT - qPt.ApexRT);
if (currDiff < timeDiff)
{
timeDiff = currDiff;
holdStandard = standard;
}
}
return(holdStandard);
}
return(null);
}
public static void GetInternalStandards(Dictionary <int, Batch> batchDict, SQLiteConnection conn)
{
List <int> returnList = new List <int>();
var queryText = "SELECT s.GroupID FROM GCMaster_FeatureGroup_Table s WHERE s.IsInternalStandard=1";
var queryCommand = new SQLiteCommand(queryText, conn);
var reader = queryCommand.ExecuteReader();
while (reader.Read())
{
var id = int.Parse(reader["GroupID"].ToString());
returnList.Add(id);
}
List <double> internalStandardIntensities = new List <double>();
foreach (var id in returnList)
{
//go find that id in each replicate and make a new internal standard, also add the intensity to a list
foreach (var batch in batchDict.Values)
{
foreach (var rep in batch.replicates)
{
if (rep.quantDictionary.ContainsKey(id))
{
var internalStandardFeature = rep.quantDictionary[id];
internalStandardIntensities.Add(internalStandardFeature.ApexIntensity);
var newInternalStandard = new InternalStandard();
newInternalStandard.ApexIntensity = rep.quantDictionary[id].ApexIntensity;
newInternalStandard.ApexRT = internalStandardFeature.ApexRT;
newInternalStandard.GCMasterGroup_ID = id;
newInternalStandard.ReplicateName = rep.name;
newInternalStandard.Feature_ID = internalStandardFeature.FeatureID;
rep.internalStandards.Add(newInternalStandard);
}
}
}
internalStandardIntensities = internalStandardIntensities.OrderBy(x => x).ToList();
var median = internalStandardIntensities.Median();
foreach (var batch in batchDict.Values)
{
foreach (var rep in batch.replicates)
{
foreach (var internalStandard in rep.internalStandards)
{
if (internalStandard.GCMasterGroup_ID == id)
{
internalStandard.CorrectionFactor = median / internalStandard.ApexIntensity;
}
}
}
}
}
foreach (var batch in batchDict.Values)
{
foreach (var rep in batch.replicates)
{
foreach (var key in rep.quantDictionary.Keys)
{
var qPt = rep.quantDictionary[key];
var nearestStandard = GetClosestInternalStandard(qPt, rep.internalStandards);
if (nearestStandard != null)
{
qPt.ApexIntensity_Normalized = qPt.ApexIntensity * nearestStandard.CorrectionFactor;
}
else
{
}
}
}
}
foreach (var batch in batchDict.Values)
{
HashSet <int> keys = new HashSet <int>();
foreach (var rep in batch.replicates)
{
foreach (var key in rep.quantDictionary.Keys)
{
keys.Add(key);
}
}
foreach (var key in keys)
{
var currAvgPt = batch.avgQuantDict[key];
List <double> normalizedPts = new List <double>();
foreach (var rep in batch.replicates)
{
if (rep.quantDictionary.ContainsKey(key))
{
var normalizedPt = rep.quantDictionary[key].ApexIntensity_Normalized;
if (normalizedPt != 0)
{
normalizedPts.Add(normalizedPt);
}
}
}
if (normalizedPts.Count > 0)
{
currAvgPt.Allintensities_Normalized = normalizedPts;
currAvgPt.AvgIntensity_Normalized = normalizedPts.Average();
currAvgPt.AvgIntensity_Normalized_StdDev = normalizedPts.StandardDeviation();
}
}
}
foreach (var batch in batchDict.Values)
{
if (batch.control != null)
{
var controlBatch = batch.control;
List <int> validKeys = controlBatch.avgQuantDict.Keys.Where(x => batch.avgQuantDict.ContainsKey(x)).ToList();
foreach (var key in validKeys)
{
var avgValLessControl = batch.avgQuantDict[key].AvgIntensity_Normalized - controlBatch.avgQuantDict[key].AvgIntensity_Normalized;
batch.avgQuantDict[key].AvgIntensity_Normalized_LessControl = avgValLessControl;
// batch.avgQuantDict[key].AvgIntensity_LessControl_PValue = Statistics.GetWelchsTTestPValue(batch.avgQuantDict[key].AllIntensities, controlBatch.avgQuantDict[key].AllIntensities);
var pVal = Statistics.GetWelchsTTestPValue(batch.avgQuantDict[key].Allintensities_Normalized, controlBatch.avgQuantDict[key].Allintensities_Normalized);
pVal = Math.Pow(10, -pVal);
batch.avgQuantDict[key].AvgIntensity_Normalized_LessControl_PValue = pVal;
}
}
}
}
