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Blocks

A block method, or short "block", is an R function that encapsulates a complete analysis sequence of statistical methods, e.g. CRMAv2.  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 CRMAv1.
    Chip types: Only Affymetrix 10K-500K SNP chip types.
    Comment: We recommend to use CRMAv2 instead.
  • doCRMAv2() / doASCRMAv2() - Total and/or allele-specific copy numbers using CRMAv2.
    Chip types: Any Affymetrix SNP & CN chip types (10K-GWS6).
  • doRMA() - RMA preprocessing and probe summarization of Affymetrix gene expression arrays.
  • doGCRMA() - gcRMA preprocessing and probe summarization of Affymetrix gene expression arrays.
More blocks will be introduced over time, e.g. doFIRMA().