maPreproc: Preprocessing of microarray expression data
In GSEABenchmarkeR: Reproducible GSEA Benchmarking

Description Usage Arguments Value Author(s) See Also Examples

This function prepares datasets of the GEO2KEGG microarray compendium for further analysis. This includes summarization of probe level expression to gene level expression as well as annotation of required colData slots for sample grouping.

1	maPreproc(exp.list, parallel = NULL)

`exp.list`	Experiment list. A `list` of datasets, each being of class `ExpressionSet`.
`parallel`	Parallel computation mode. An instance of class `BiocParallelParam`. See the vignette of the `BiocParallel` package for switching between serial, multi-core, and grid execution. Defaults to `NULL`, which then uses the first element of `BiocParallel::registered()` for execution. If not changed by the user, this accordingly defaults to multi-core execution on the local host.

A list of datasets, each being of class SummarizedExperiment.

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

loadEData to load a specified expression data compendium.

    # reading user-defined expression data from file
    geo2kegg <- loadEData("geo2kegg", nr.datasets=3)

    # only considering the first 100 probes for demonstration
    geo2kegg <- lapply(geo2kegg, function(d) d[1:100,])   

    # preprocessing two datasets
    geo2kegg <- maPreproc(geo2kegg[2:3])