NEWS

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proBatch 2.2.0

NEW FEATURES

• Added design and metadata diagnostics, grouped missing-value filtering and plots, and t-SNE and UMAP plots for matrices and ProBatchFeatures.
• Added unified long/wide centering and batch correction, plus provider-aware registered transformations for ProBatchFeatures.

SIGNIFICANT USER-VISIBLE CHANGES

• Batch correction now errors on missing values by default; use "keep", "drop_features", or "fill" explicitly. Invalid or conflicting identifiers, assay selections, lineage, and result names now also error.

DEPRECATED

• Deprecated center_feature_batch_medians_df(), center_feature_batch_means_df(), center_feature_batch_medians_dm(), center_feature_batch_means_dm(), correct_with_ComBat_df(), correct_with_ComBat_dm(), correct_batch_effects_df(), correct_batch_effects_dm(), and correct_with_removeBatchEffect_dm(); use center_feature_batch(), correct_with_ComBat(), correct_batch_effects(), or correct_with_removeBatchEffect().

BUG FIXES

• Fixed edge cases in batch correction, sample matching, CV and nonlinear fitting, date parsing, and diagnostic plots.

proBatch 1.99.0

NEW FEATURES

• Added ProBatchFeatures support, including multiple assays and feature levels, across correction and plotting functions.
• Added limma batch correction and missing-value heatmap, density, and frequency plots for ProBatchFeatures objects.

proBatch 1.1.0

NEW FEATURES

• Added matrix and long-format transformation APIs with sample consistency checks and preservation of original long-format measurements.
• Added generic heatmaps and consistent missing-value and colour handling across diagnostic plots.

SIGNIFICANT USER-VISIBLE CHANGES

• Renamed center_peptide_batch_medians() to center_feature_batch_medians(), normalize_custom_fit() to adjust_batch_trend(), and plot_heatmap() to plot_heatmap_diagnostic().