SampleSet is an S4 class defined for the purpose of running the funtooNorm algorithm. They are lists containing signal data and different variables useful for funtooNorm. The data is separated into the 3 probes types, each having 2 channels (methylated and unmethylated ie : A and B) We then define then the 6 (2*3) labels: AIGrn BIGrn AIRed BIRed AII BII
a S4 object of class SampleSet
Character: is 'minfi' or 'GenomeStudio'
character vector: contain the list of sample names in order used
numeric: the number of samples
numeric: the number of positions in the ILLUMINA chip
character: the annotation object from minfi package
factor: vector of the cell type for each sample as factors
numeric: vector of ordered quantiles
list: list of 6 quantiles tables for the 6 signal types
matrix: covariance matrix for the model fit
list: list of the values for all 6 probe types.
list: list of probes for each type
list: list of the normalized values for all 6 probe types.
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