Primer: Preparing NChannelSet objects with differential expression scores

The gCMAP package offers a the generate_gCMAP_NChannelSet function to process multiple instances differential expression experiments with two classes (e.g. cases vs controls). For microarray data, the limma package is used to calculate a moderated t-statistic (default). Optionally, a standard t-test can be computed instead. For RNAseq data, the DESeq package is used instead. Data preprocessing differs considerably between different technologies and array platforms and needs to be performed beforehand. Normalized microarray data and accompanying annotation is passed to generate_gCMAP_NChannelSet as a list of ExpressionSet objects, RNAseq data can be passed as a list of CountDataSet objects instead. To generate a set of 3 example CountDataSets , we use the makeExampleCountDataSet function from the DESeq package.