Blocks

A block method, or short "block", is an R function that encapsulates a complete analysis sequence of statistical methods, e.g. CRMA v2. Blocks are recognized by their prefix do-, e.g. doCRMAv2(). These are provided for convenience, and although they do not give all the flexibility as a custom-made script, they do support the most commonly used use cases.

Available blocks:

• doCRMAv1() / doASCRMAv1() - Total and/or allele-specific copy numbers using CRMA v1.
  Chip types: Only Affymetrix 10K-500K SNP chip types.
  Comment: We recommend to use CRMA v2 instead.
• doCRMAv2()` / doASCRMAv2() - Total and/or allele-specific copy numbers using CRMA v2.
  Chip types: Any Affymetrix SNP & CN chip types (10K-GWS6).
• doFIRMA() - FIRMA preprocessing, probe summarization, and alternative splicing estimation on Affymetrix exon arrays.
• doGCRMA() - GCRMA preprocessing and probe summarization on Affymetrix gene expression arrays.
• doRMA() - RMA preprocessing and probe summarization on Affymetrix gene expression arrays.
  Chip types: Any Affymetrix chip types.