Hello,
I was wondering if you could help with the following error:
System.IO.InvalidDataException: Insufficient target peaks (0 with 5718 decoys) detected at 15% FDR to continue training. ---> System.IO.InvalidDataException: Insufficient target peaks (0 with 5718 decoys) detected at 15% FDR to continue training.
at pwiz.Skyline.Model.Results.Scoring.MProphetPeakScoringModel.CalculateWeights(String documentPath, ScoredGroupPeaksSet targetTransitionGroups, ScoredGroupPeaksSet decoyTransitionGroups, Boolean includeSecondBest, Boolean nonParametricPValues, Double qValueCutoff, Double[] weights, Double& decoyMean, Double& decoyStdev, Boolean& colinearWarning) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\Scoring\MProphetScoringModel.cs:line 405
at pwiz.Skyline.Model.Results.Scoring.MProphetPeakScoringModel.<>c__DisplayClass7.<Train>b__4(MProphetPeakScoringModel im) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\Scoring\MProphetScoringModel.cs:line 255
at pwiz.Common.SystemUtil.Immutable.ChangeProp[TIm](TIm immutable, SetLambda1 set) in c:\proj\pwiz_x64\pwiz_tools\Shared\Common\SystemUtil\Immutable.cs:line 201 at pwiz.Skyline.Model.Results.Scoring.MProphetPeakScoringModel.Train(IList
1 targetsIn, IList1 decoysIn, LinearModelParams initParameters, Nullable
1 iterations, Boolean includeSecondBest, Boolean preTrain, IProgressMonitor progressMonitor, String documentPath) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\Scoring\MProphetScoringModel.cs:line 196
at pwiz.Skyline.SettingsUI.EditPeakScoringModelDlg.<>c__DisplayClass13.<TrainModel>b__b(IProgressMonitor progressMonitor) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\EditPeakScoringModelDlg.cs:line 269
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 228 --- End of inner exception stack trace --- at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1842 at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action
1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 176
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 131
at pwiz.Skyline.SettingsUI.EditPeakScoringModelDlg.TrainModel(Boolean suppressWeights) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\EditPeakScoringModelDlg.cs:line 272
at pwiz.Skyline.SettingsUI.EditPeakScoringModelDlg.TrainModelClick() in c:\proj\pwiz_x64\pwiz_tools\Skyline\SettingsUI\EditPeakScoringModelDlg.cs:line 191
The Skyline file contains 447 target proteins with the same number of decoys (shuffled sequence).
When performing -> Reintegrate -> Peak scoring, it gives error when mprophet option is used, default is fine but then Skyline integrated MSstats gives an error as it is also missing q-values:
** Reading the data for MSstats.....
** iRT proteins/peptides are removed.
Peptides, that are used in more than one proteins, are removed.
** Truncated peaks are replaced with NA.
** For DDA datasets, three isotopic peaks per feature and run are summed.
Error in SkylinetoMSstatsFormat(raw, filter_with_Qvalue = filter.qvalue) :
** Please check annotation for Condition and BioReplicat column. There is missing information.
Can't finish analysis.
What can i do?
Many thanks,
Silvia