public NormalizationData GetNormalizationData() { if (_normalizationData == null) { _normalizationData = _getNormalizationDataFunc(); } return(_normalizationData); }
public NormalizationData GetNormalizationData() { if (_normalizationData == null) { _normalizationData = NormalizationData.GetNormalizationData(SrmDocument, ComparisonDef.UseZeroForMissingPeaks, ComparisonDef.QValueCutoff); } return(_normalizationData); }
public NormalizationData GetNormalizationData() { if (!NormalizationMethod.EQUALIZE_MEDIANS.Equals(ComparisonDef.NormalizationMethod)) { return(null); } return(_normalizationData = _normalizationData ?? NormalizationData.GetNormalizationData(SrmDocument)); }
public static PeptideQuantifier GetPeptideQuantifier(SrmDocument document, PeptideGroupDocNode peptideGroup, PeptideDocNode peptide) { return(GetPeptideQuantifier(() => NormalizationData.GetNormalizationData(document, false, null), document.Settings, peptideGroup, peptide)); }
private Quantity GetTransitionQuantity( SrmSettings srmSettings, IDictionary <PeptideDocNode.TransitionKey, TransitionChromInfo> peptideStandards, int replicateIndex, TransitionGroupDocNode transitionGroup, TransitionDocNode transition) { if (null == transition.Results) { return(null); } if (replicateIndex >= transition.Results.Count) { return(null); } var chromInfos = transition.Results[replicateIndex]; if (null == chromInfos) { return(null); } var chromInfo = GetTransitionChromInfo(transition, replicateIndex); if (null == chromInfo || chromInfo.IsEmpty) { return(null); } double normalizedArea = chromInfo.Area; double denominator = 1.0; if (null != peptideStandards) { TransitionChromInfo chromInfoStandard; if (!peptideStandards.TryGetValue(GetRatioTransitionKey(transitionGroup, transition), out chromInfoStandard)) { return(null); } else { denominator = chromInfoStandard.Area; } } else { if (chromInfo.IsTruncated.GetValueOrDefault()) { return(null); } if (Equals(NormalizationMethod, NormalizationMethod.GLOBAL_STANDARDS)) { denominator = srmSettings.CalcGlobalStandardArea(replicateIndex, chromInfo.FileId); } else if (Equals(NormalizationMethod, NormalizationMethod.EQUALIZE_MEDIANS)) { if (null == NormalizationData) { throw new InvalidOperationException(string.Format("Normalization method '{0}' is not supported here.", NormalizationMethod)); // Not L10N } double?median = NormalizationData.GetMedian(chromInfo.FileId, transitionGroup.TransitionGroup.LabelType); if (!median.HasValue) { return(null); } denominator = Math.Pow(2.0, median.Value); } } return(new Quantity(normalizedArea, denominator)); }