NACHO

NACHO provides quality control and preprocessing for NanoString nCounter targeted gene expression data.

Key Features:

• Summarize–Visualize–Normalize pipeline: Integrates three explicit steps—summarize, visualize, and normalize—specific to NanoString nCounter data.
• Summarize: Collects and organizes input data into a tidy format to prepare datasets for QC and downstream analysis.
• Visualize: Calculates and visualizes key QC metrics including manufacturer's default QC measures and additional metrics, and generates plots of control-gene expression and principal components analysis (PCA).
• Normalize: Calculates scaling factors and offers multiple normalization methods to preprocess nCounter expression data for downstream analyses.

Scientific Applications:

• QC of nCounter experiments: Assess sample and assay quality for NanoString nCounter targeted expression experiments using manufacturer and additional QC metrics.
• Control-gene and PCA assessment: Evaluate technical variation and sample relationships via control-gene expression plots and principal components analysis.
• Preprocessing for downstream analysis: Apply scaling-factor–based normalization to prepare targeted gene expression data from biofluids and tissues for differential expression or other analyses.

Methodology:

Collect and organize data into a tidy format; compute manufacturer's default and additional QC metrics; generate control-gene expression plots and perform PCA; calculate scaling factors and apply selected normalization methods.