Introduction | Important Terminology | Within- and between-product bridging | Considerations for between-product bridging | Bridge Sample Selection | Workflow Overview | Import NPX files | Checking input datasets and bridging samples | Normalization | Determining bridging recommendations | Normalization using the median of paired differences | Quantile smoothing | Function Output | Evaluating the quality of bridging | Exporting Normalized Data | FAQs | Overlapping Assays within products | Downstream Analysis | Contact Us | Legal Disclaimer

Introduction | Integrating LOD | Import Olink NGS datasets | A note on calculating LOD with clean_npx() | Integrating Negative Control LOD | A note on calculating LOD from counts | Integrating Fixed LOD | When to Use Fixed LOD vs NC LOD | Integrating Both NC LOD and Fixed LOD | Adjusting LOD for Intensity Normalized Data | Handling LOD in Bridge-Normalized Data | Export Olink NGS Data with LOD | Contact Us | Legal Disclaimer

Selecting bridge samples | Setup bridging datasets | Check bridging datasets | Bridging between two data sets | Perform bridging with non-matching sample names | Bridging evaluation | Export Bridged data | Contact Us | Legal Disclaimer

Introduction | PCA Plot | Overview of PCA Plot | How to use PCA plot to identify an outlier | PCA plot by panel | Labeling outliers | NPX Distribution Plot | Overview of NPX Distribution Plot | How to use NPX distribution plot to identify an outlier | QC Plot (IQR vs Sample Median) | Overview of QC Plot | How to use QC plot to identify an outlier | Interpreting and Handling Outliers | When should outliers be removed | Contact Us | Legal Disclaimer

Introduction | Sample randomization | Complete randomization | Generate randomization scheme that keeps subjects on the same plate | Multi-study manifests | Visualization | Plate layouts | Plate distribution | Data Output | Contact Us | Legal Disclaimer

Introduction | Important Terminology | Within- and between-product bridging | Considerations for between-product bridging | Bridge Sample Selection | Workflow Overview | Import NPX files | Checking input datasets and bridging samples | Normalization | Determining bridging recommendations | Normalization using the median of paired differences | Quantile smoothing | Function Output | Evaluating the quality of bridging | Exporting Normalized Data | FAQs | Overlapping Assays within products | Downstream Analysis | Contact Us | Legal Disclaimer

Introduction | Integrating LOD | Import Olink NGS datasets | A note on calculating LOD with clean_npx() | Integrating Negative Control LOD | A note on calculating LOD from counts | Integrating Fixed LOD | When to Use Fixed LOD vs NC LOD | Integrating Both NC LOD and Fixed LOD | Adjusting LOD for Intensity Normalized Data | Handling LOD in Bridge-Normalized Data | Export Olink NGS Data with LOD | Contact Us | Legal Disclaimer

Selecting bridge samples | Setup bridging datasets | Check bridging datasets | Bridging between two data sets | Perform bridging with non-matching sample names | Bridging evaluation | Export Bridged data | Contact Us | Legal Disclaimer

Introduction | PCA Plot | Overview of PCA Plot | How to use PCA plot to identify an outlier | PCA plot by panel | Labeling outliers | NPX Distribution Plot | Overview of NPX Distribution Plot | How to use NPX distribution plot to identify an outlier | QC Plot (IQR vs Sample Median) | Overview of QC Plot | How to use QC plot to identify an outlier | Interpreting and Handling Outliers | When should outliers be removed | Contact Us | Legal Disclaimer

Introduction | Sample randomization | Complete randomization | Generate randomization scheme that keeps subjects on the same plate | Multi-study manifests | Visualization | Plate layouts | Plate distribution | Data Output | Contact Us | Legal Disclaimer

Installation | List of functions | Usage | Introduction to Olink NPX data format | Preprocessing | Read NPX data (read_NPX) | Function arguments | Function output | Read multiple NPX data files (read_NPX) | Check NPX data quality (check_npx) | Clean NPX data (clean_npx) | Randomize samples on plate (olink_plate_randomizer) | Select bridge samples (olink_bridgeselector) | Normalizing NPX data (olink_normalization) | Integrating Explore NPX LOD (olink_lod) | Statistical analysis | T-test analysis (olink_ttest) | Mann-Whitney U Test analysis (olink_wilcox) | Analysis for variance (ANOVA) (olink_anova) | Post-hoc ANOVA analysis (olink_anova_posthoc) | Linear mixed effects model analysis (olink_lmer) | Function outcome | Post-hoc linear mixed effects model analysis (olink_lmer_posthoc) | Additional Statistical Tests | Pathway Enrichment (olink_pathway_enrichment) | Function Arguments | Function Output | Exploratory analysis | Principal components analysis (PCA) plot (olink_pca_plot) | Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) (olink_umap_plot) | Function arguments (selection) | Visualization | Boxplots for outcomes (olink_boxplot) | Boxplots for QC (olink_dist_plot) | Point-range plot for LMER (olink_lmer_plot) | Heatmap for visualizing pathway enrichment (olink_pathway_heatmap) | Bargraph for visualizing pathway enrichment (olink_pathway_visualization) | Scatterplot for QC (olink_qc_plot) | Heatmap (olink_heatmap_plot) | Plot results of t-test (olink_volcano_plot) | Theming function (set_plot_theme) | Color theming (olink_color_discrete, olink_color_gradient, olink_fill_discrete, olink_fill_gradient) | Visualizing bridgeability criteria for between-product normalization (olink_bridgeability_plot) | Contact Us | Legal Disclaimer