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Welcome to the MultiAssayExperiment wiki!

To access our API, please go to MultiAssayExperiment API

http://cran.r-project.org/web/packages/cgdsr/vignettes/cgdsr.pdf looks relevant in various respects

Some brainstorming on design objectives for the MultiAssay object:

Project Objectives

1. Store multiple assays associated with overlapping sets of specimens, along with metadata, in a single object
2. Allow operations that are familiar to users of the ExpressionSet, e.g. exprs(), obj[, subset]. These should work even if some samples are missing from some assays.
3. Allow storage of assay-specific sample metadata, in addition to experiment-wide sample metadata. This might be useful for error-checking by the analyst when samples are given different IDs in each assay, other than the primary specimen identifer.
4. Allow that different assays may be represented by different features
   • Somehow facilite the creation of "maps" between assays? e.g. genes and putative microRNA regulators, or genes and their transcription factors?
5. Allow, but don't require, the use of Genomic Ranges in assay data
6. Simplify tasks such as:
   • selecting samples which meet specified criteria on the metadata
   • selecting samples for which desired assays are available
7. Allow the creation of methods and functions for common multi-assay genomic computations, e.g.:
   • correlation between expression and copy number
   • correlation between expression and putative microRNA regulators,
   • AND/OR across assays, e.g. identifying in which samples a gene/genes are methylated OR mutated OR deleted.