Changes in version 1.23.2 o remove deprecated stato classes; use ontology slots instead Changes in version 1.23.1 o general maintenance o fix PLSDA probability calculation Changes in version 1.19.2 o fix pca_biplot Changes in version 1.19.1 o fix ANOVA output with interaction terms Changes in version 1.15.2 o fix ANOVA type 1 o add control_group param to ttest Changes in version 1.13.5 o improve consistency between methods in fold change computations o better handling of NA in fold change computations Changes in version 1.13.4 o fix PLSDA predicted group assignment o add option to PLSDA to use probability for yhat for predictions o update tests Changes in version 1.13.3 o d-ratio equations changed to match Broadhurst et al (2018) o add tests for d-ratio o fix PCA eigenvalues calculation Changes in version 1.13.2 o d-ratio filter now correctly removes features o update descriptions/documentation for missing value filters o add tests for d-ratio Changes in version 1.13.1 o hotfix vector_norm now correctly normalises samples to length 1 o re-sync with Bioc devel o fix broken documentation Changes in version 1.7.2 o internal updates to PLS o some PLS charts have been renamed for consistency with other methods Changes in version 1.6.1 o hotfix vector_norm now correctly normalises samples to length 1 o added vector_norm_tests Changes in version 1.5.7 o improve NA handling in fold_change computations Changes in version 1.5.5 o change t-test outputs to data.frame o fix NA bug in feature_boxplot chart o use new ontology system in place of stato Changes in version 1.5.2 o add outputs to auto-generated documentation o fix fold change threshold using median (#56) o add fold change using means (#57) o HSD param "unbalanced" is no longer ignored Changes in version 1.5.1 o fixed broken paired tests Changes in version 1.4.2 o fix fold change threshold using median (#56) o HSD param "unbalanced" is no longer ignored Changes in version 1.4.1 o fixed broken paired tests Changes in version 1.4.0 o added VIP summary chart o add ellipse plotting options to pca_scores_plot o mv_sample_filter can be used in train/predict mode o Documentation updates o Minor issue fixes o Add median method for fold change o Update PQN with new inputs/outputs due to changes in pmp package o Update SBC with new inputs/outputs due to changes in pmp package o Update MTBLS79 due to changes in SBC Changes in version 1.1.2 o Documentation updates o Bug fixes Changes in version 1.0.1 o Fix HCA bug Changes in version 1.0.0 o Bioconductor 3.11 release Changes in version 0.99.10 o add Metabolmics BiocView o fix missing sections at end of vignette Changes in version 0.99.9 o add proteomics vignette o add mean_of_medians o merge all vignettes o fix bug in kfold_xval_grid Changes in version 0.99.8 o added stratified splitting (stratified_split) o added Gastric Cancer vignette o add AUC metric o add predicted and ROC plots for PLSDA Changes in version 0.99.7 o minor documentation updates Changes in version 0.99.6 o fix issues using class() due to changes in R 4.0.0 Changes in version 0.99.5 o fix dimnames mismatch for knn-impute o add additional vignettes Changes in version 0.99.4 o Add SVM, nroot transform, constant sum norm o Add funtionality to autoscaling o Fix some issues with permutation testing of model sequences o Add option to impute by samples to knn o Add custom feature labels option to pca loadings Changes in version 0.99.3 o Fix dimnames mismatch errors o Updated struct depency to 0.99.5 Changes in version 0.99.2 o renamed some charts containing .'s to use underscores o renamed sbcms dataset to MTBLS79 Changes in version 0.99.1 o minor updates to pass Bioconductor checks Changes in version 0.99.0 o use new struct v0.99.4 class constructor functions Changes in version 0.8.4 o Final working version befor bioconductor updates Changes in version 0.4.0 (2019-07-25) o Minor bug fixes o Added tsne method o Added sbcms dataset o Added methods related to signal/batch correction