RGChannelSet

RGChannelSet is an S4 class used in Bioconductor to represent two-color microarray data, capturing the raw intensities of the red and green channels for a set of features across multiple samples. It typically includes matrices of red and green channel intensities along with optional feature and sample annotations, and may also store background measurements and control features.

Creation and representation: The RGChannelSet is usually produced by functions such as read.maimages from the limma package, which reads two-color array data and stores the red and green channel measurements in a structured object. It provides convenient access to the two channel values and their associated metadata, enabling downstream processing without reconstructing the data from plaintext files.

Usage in analysis workflows: In typical workflows, researchers use the RGChannelSet as input for normalization and summarization steps in two-color microarray analysis. After optional background correction, within-array and between-array normalization can be applied to the red and green channels. Derived quantities such as M = log2(R) − log2(G) and A = (log2(R) + log2(G)) / 2 can be computed for further analysis. The object then feeds into linear modeling and differential expression analysis via limma’s modeling functions (for example, lmFit and eBayes).

Relation to other data structures: RGChannelSet is part of a family of representations for two-color data in Bioconductor. It is often contrasted with older representations like RGList and with newer SummarizedExperiment-based workflows, which may be used in broader integrative analyses. The RGChannelSet remains a standard, well-supported container for raw two-color array data within limma workflows.