Vignettes

DNA genotyping & copy number analysis

Copy-number preprocessing:

• CRMA (v2): Estimation of total copy numbers using the CRMA v2 method (10K-CytoScanHD)
• CRMA (v1): Total copy number analysis using CRMA v1 (10K, 100K, 500K)
• ACNE: Allele-specific copy numbers using non-negative matrix factorization
• CalMaTe - A calibration method to improve allele-specific copy number estimates from SNP microarrays
• TumorBoost - Normalization of allelic-specific copy numbers in tumors with matched normals
• TumorBoost - Normalization of allelic-specific copy numbers in tumors with matched normals (low-level API)
• CRMA (v2): Paired total copy number analysis
• CRMA (v1&v2): Sex-chromosome bias-corrected reference signals from pooled average
• Calculating raw total copy numbers manually

Copy-number segmentation:

• Total copy-number segmentation (non-paired CBS)
• Paired parent-specific copy-number segmentation (Paired PSCBS) (low-level API after ASCRMAv2)

Integrating copy numbers from multiple platforms:

• MSCN: Multi-source copy-number normalization
• MSCN: Creating binary data files containing copy number estimates

Genotyping:

• CRLMM genotyping (100K and 500K)

Deprecated (=do not use):

• Total Copy Number Analysis (GWS5 & GWS6) [DEPRECATED]
• CRMA (v1&v2): Paired total copy number analysis (old version) [DEPRECATED]

RNA expression analysis

• RMA: Gene 1.0 ST array analysis
• FIRMA: Human exon array analysis
• FIRMA: Using the GenomeGraphs package with FIRMA

Tiling array analysis

• MAT: Tiling array analysis (Promoter 1.0R)

Miscellaneous

• Empirical probe-signal densities and rank-based quantile normalization