public static Batch GetMedianReferenceExperiment(Dictionary <int, Batch> batchDictionary)
{
Batch returnBatch = new Batch();
HashSet <int> allIds = new HashSet <int>();
foreach (var batch in batchDictionary.Values)
{
foreach (var rep in batch.replicates)
{
foreach (var key in rep.quantDictionary.Keys)
{
allIds.Add(key);
}
}
}
foreach (var key in allIds.ToList())
{
List <double> allMeasurements = new List <double>();
foreach (var batch in batchDictionary.Values)
{
foreach (var rep in batch.replicates)
{
if (rep.quantDictionary.ContainsKey(key))
{
allMeasurements.Add(rep.quantDictionary[key].ApexIntensity_Normalized);
}
}
}
var avgIntensity = allMeasurements.Median();
var avgPoint = new AvgQuantPoint();
avgPoint.AvgIntensity = avgIntensity;
returnBatch.avgQuantDict.Add(key, avgPoint);
}
return(returnBatch);
}
public static void GetAveragedIntensityValues(Dictionary <int, Batch> batchDict)
{
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 avgQuantPt = new AvgQuantPoint();
avgQuantPt.GCMasterGroupID = key;
foreach (var rep in batch.replicates)
{
if (rep.quantDictionary.ContainsKey(key))
{
avgQuantPt.AllIntensities.Add(rep.quantDictionary[key].ApexIntensity);
avgQuantPt.BatchID = batch.batchID;
avgQuantPt.ControlID = batch.controlID;
avgQuantPt.GCMasterGroup_ApexRT = rep.quantDictionary[key].ApexRT;
avgQuantPt.Name = rep.quantDictionary[key].Name;
avgQuantPt.ChEBI_ID = rep.quantDictionary[key].ChEBI_ID;
avgQuantPt.PreferredName = "";
if (!string.IsNullOrEmpty(avgQuantPt.Name))
{
avgQuantPt.PreferredName = avgQuantPt.Name + " | ";
}
if (avgQuantPt.ChEBI_ID != 0)
{
avgQuantPt.PreferredName += "ChEBI ID: " + avgQuantPt.ChEBI_ID + " | ";
}
avgQuantPt.PreferredName += "Apex RT: " + Math.Round(avgQuantPt.GCMasterGroup_ApexRT, 4);
}
}
avgQuantPt.AvgIntensity = avgQuantPt.AllIntensities.Average();
avgQuantPt.AvgIntensity_StdDev = avgQuantPt.AllIntensities.StandardDeviation();
avgQuantPt.AvgIntensity_Normalized_StdDev = avgQuantPt.AllIntensities.StandardDeviation();
avgQuantPt.AvgIntensity_Normalized = avgQuantPt.AllIntensities.Average();
batch.avgQuantDict.Add(key, avgQuantPt);
}
}
}
