├── README.md ├── package ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R │ ├── ALL_BEA_objects.R │ ├── BEA_Assessments.R │ ├── BEA_AssessmentsAPI.R │ ├── BEA_AssessmentsBatchcorr.R │ ├── BEA_AssessmentsBoxplot.R │ ├── BEA_AssessmentsCDP.R │ ├── BEA_AssessmentsHierclust.R │ ├── BEA_AssessmentsMANOVA.R │ ├── BEA_AssessmentsPca.R │ ├── BEA_AssessmentsPca_dsc.R │ ├── BEA_AssessmentsPca_pvalueDsc.R │ ├── BEA_AssessmentsSupervisedClust.R │ ├── BEA_CorrectionsAN.R │ ├── BEA_CorrectionsAPI.R │ ├── BEA_CorrectionsEB.R │ ├── BEA_CorrectionsEBNP.R │ ├── BEA_CorrectionsEBNPapi.R │ ├── BEA_CorrectionsEBNPdata.R │ ├── BEA_CorrectionsEBNplus.R │ ├── BEA_CorrectionsMP.R │ ├── BEA_CorrectionsRBN.R │ ├── BEA_CorrectionsRBNapi.R │ ├── BatchEffAssess.R │ ├── FilesAndDirs.R │ ├── Logging.R │ ├── ReadRJava.R │ └── zzz.R ├── inst │ ├── BoxplotJava │ │ ├── BoxplotJava.jar │ │ ├── LegendJava.jar │ │ ├── commons-lang3-3.3.2.jar │ │ ├── commons-math3-3.3.jar │ │ ├── jcommon-1.0.17.jar │ │ └── jfreechart-1.0.14.jar │ ├── DscJava │ │ ├── DscJava.jar │ │ ├── commons-lang3-3.1.jar │ │ └── commons-math3-3.3.jar │ ├── LegendJava │ │ ├── LegendJava.jar │ │ ├── jcommon-1.0.17.jar │ │ └── jfreechart-1.0.14.jar │ ├── ReadRJava │ │ └── ReadRJava.jar │ ├── doc │ │ ├── MBatch_04-06_PCA_DualBatch_Structures.R │ │ ├── MBatch_04-06_PCA_DualBatch_Structures.Rmd │ │ ├── MBatch_04-06_PCA_DualBatch_Structures.pdf │ │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.R │ │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.Rmd │ │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.pdf │ │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.R │ │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.Rmd │ │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.pdf │ │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.R │ │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.Rmd │ │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.pdf │ │ ├── MBatch_05-05_EB_withNonParametricPriors.R │ │ ├── MBatch_05-05_EB_withNonParametricPriors.Rmd │ │ ├── MBatch_05-05_EB_withNonParametricPriors.pdf │ │ ├── MBatch_05-06_EB_withParametricPriors.R │ │ ├── MBatch_05-06_EB_withParametricPriors.Rmd │ │ ├── MBatch_05-06_EB_withParametricPriors.pdf │ │ ├── MBatch_05-07_MP_Overall.R │ │ ├── MBatch_05-07_MP_Overall.Rmd │ │ ├── MBatch_05-07_MP_Overall.pdf │ │ ├── MBatch_05-08_MP_ByBatch.R │ │ ├── MBatch_05-08_MP_ByBatch.Rmd │ │ ├── MBatch_05-08_MP_ByBatch.pdf │ │ ├── MBatch_05-09_AN_Adjusted.R │ │ ├── MBatch_05-09_AN_Adjusted.Rmd │ │ ├── MBatch_05-09_AN_Adjusted.pdf │ │ ├── MBatch_05-10_AN_Unadjusted.R │ │ ├── MBatch_05-10_AN_Unadjusted.Rmd │ │ ├── MBatch_05-10_AN_Unadjusted.pdf │ │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.R │ │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.Rmd │ │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.pdf │ │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.R │ │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.Rmd │ │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.pdf │ │ ├── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.R │ │ ├── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.Rmd │ │ └── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.pdf │ └── gpl-2_0.txt ├── man │ ├── AN_Adjusted.Rd │ ├── AN_Unadjusted.Rd │ ├── BEA_DATA-class.Rd │ ├── Boxplot_AllSamplesData_Structures.Rd │ ├── Boxplot_AllSamplesRLE_Structures.Rd │ ├── Boxplot_Group_Structures.Rd │ ├── CDP_Files.Rd │ ├── CDP_Plot.Rd │ ├── CDP_Structures.Rd │ ├── EBNPlus_CheckData_Structures.Rd │ ├── EBNPlus_CombineBatches.Rd │ ├── EBNPlus_Correction_Files.Rd │ ├── EBNPlus_Correction_Structures.Rd │ ├── EBNPlus_TrainAndValidateFromVector_Structures.Rd │ ├── EBNPlus_TrainAndValidateReplicates_Structures.Rd │ ├── EB_withNonParametricPriors.Rd │ ├── EB_withParametricPriors.Rd │ ├── HierarchicalClustering_Structures.Rd │ ├── Logging-class.Rd │ ├── MP_ByBatch.Rd │ ├── MP_Overall.Rd │ ├── PCA_DualBatch_Structures.Rd │ ├── PCA_Regular_Structures.Rd │ ├── RBN_Pseudoreplicates.Rd │ ├── RBN_Replicates.Rd │ ├── SupervisedClustering_Batches_Structures.Rd │ ├── SupervisedClustering_Pairs_Structures.Rd │ ├── buildDSCOverviewFile.Rd │ ├── clearDSCOverviewFiles.Rd │ ├── getReplicatesForRBN.Rd │ ├── mbatchFilterData.Rd │ ├── mbatchIncludeExcludeData.Rd │ ├── mbatchLoadFiles.Rd │ ├── mbatchLoadStructures.Rd │ ├── mbatchTrimData.Rd │ ├── mbatchWriteSuccessfulLog.Rd │ ├── readAsDataFrame.Rd │ ├── readAsGenericMatrix.Rd │ ├── readAsMatrix.Rd │ ├── setLogging.Rd │ ├── writeAsDataframe.Rd │ └── writeAsMatrix.Rd ├── tests │ ├── AN_Adjusted.R │ ├── AN_Unadjusted.R │ ├── Boxplot_AllSamplesData_Structures.R │ ├── Boxplot_AllSamplesRLE_Structures.R │ ├── Boxplot_Group_Structures.R │ ├── CDP_Files.R │ ├── CDP_Plot.R │ ├── CDP_Structures.R │ ├── EBNPlus_CombineBatches.R │ ├── EBNPlus_Correction_Files.R │ ├── EBNPlus_Correction_Structures.R │ ├── EB_withNonParametricPriors.R │ ├── EB_withParametricPriors.R │ ├── HierarchicalClustering_Structures.R │ ├── MP_ByBatch.R │ ├── MP_Overall.R │ ├── PCA_DualBatch_Structures.R │ ├── PCA_Regular_Structures.R │ ├── RBN_Pseudoreplicates.R │ ├── RBN_Replicates.R │ ├── SupervisedClustering_Batches_Structures.R │ └── SupervisedClustering_Pairs_Structures.R └── vignettes │ ├── BoxPlot_AllSample-Data_Diagram-TSS.png │ ├── BoxPlot_AllSample-RLE_Diagram-BatchId.png │ ├── MBatch_04-06_PCA_DualBatch_Structures.Rmd │ ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.Rmd │ ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.Rmd │ ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.Rmd │ ├── MBatch_05-05_EB_withNonParametricPriors.Rmd │ ├── MBatch_05-06_EB_withParametricPriors.Rmd │ ├── MBatch_05-07_MP_Overall.Rmd │ ├── MBatch_05-08_MP_ByBatch.Rmd │ ├── MBatch_05-09_AN_Adjusted.Rmd │ ├── MBatch_05-10_AN_Unadjusted.Rmd │ ├── MBatch_05-11_EBNPlus_CheckData_Structures.Rmd │ ├── MBatch_05-12_EBNPlus_TrainAndValidateReplicates_Structures.Rmd │ ├── MBatch_05-13_EBNPlus_TrainAndValidateFromVector_Structures.Rmd │ ├── boxplot_dynamic.PNG │ ├── boxplot_dynamic_data.PNG │ ├── pca_plus.png │ └── supervised_clustering.png └── pdf ├── MBatch_01_InstallLinux.pdf ├── MBatch_01_InstallOSX.pdf ├── MBatch_01_InstallWindows.pdf ├── MBatch_02_RunningTests.pdf ├── MBatch_03_StandardizedData.pdf ├── MBatch_03_UserData.pdf ├── MBatch_04-00_ParametersBatchTypesValues.pdf ├── MBatch_04-01_SupervisedClusteringBatchesStructures.pdf ├── MBatch_04-02_PCA_Regular_Structures.pdf ├── MBatch_04-03_HierarchicalClustering_Structures.pdf ├── MBatch_04-04_Boxplot_Group_Structures.pdf ├── MBatch_04-05_CDP_Structures.pdf ├── MBatch_04-06_PCA_DualBatch_Structures.pdf ├── MBatch_04-07_SupervisedClustering_Pairs_Structures.pdf ├── MBatch_04-08_Boxplot_AllSamplesRLE_Structures.pdf ├── MBatch_04-09_Boxplot_AllSamplesData_Structures.pdf ├── MBatch_05-01_EBNPlus_CombineBatches.pdf ├── 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