maPreproc | R Documentation |
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.
maPreproc(exp.list, parallel = NULL)
exp.list |
Experiment list. A |
parallel |
Parallel computation mode. An instance of class
|
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])
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