Methylation Array

Imported Array Data (idat files)

Analysis tasks that can be invoked from imported idat data is listed below.

Task Menu Section	Analysis Task Name
Pre-analysis tools	Generate beta value

Beta Values Count Matrix

After signal intensities in the idat files are converted to beta values, analysis tasks listed below can be invoked.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
QA/QC	Feature distribution
Pre-analysis tools	Annotate features Generate methylation mvalues
Filtering	Filter samples Split by attribute
Statistics	Detect differential methylation Descriptive statistics
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters PCA t-SNE UMAP Hierarchical clustering / heatmap Chromosome view SVD
Conversion	Export matrix

PCA

Analysis tasks that can be invoked from PCA data node are listed below.

Task Menu Section	Analysis Task Name
Annotation/Metadata	Publish attributes to study
Batch removal	General linear model Harmony
Statistics	Differential analysis Correlation Descriptive statistics Compute biomarkers Cox Regression Kaplan-Meier
Exploratory analysis	Graph-based clustering K-means clustering Compare clusters t-SNE UMAP Find multimodal neighbors SVD
Conversion	Export matrix

Differential Analysis Result

Analysis tasks that can be invoked from differential analysis result (e.g., Detect differential methylation) are listed below.

Task Menu Section	Analysis Task Name
QA/QC	Feature distribution
Filtering	Differential analysis filter
Statistics	Descriptive statistics
Exploratory analysis	Hierarchical clustering / heatmap Chromosome view Merge differential expression results
Biological interpretation	Gene set enrichment Correlation Engine atlases Correlation Engine pathways