Normalization By Remove Unwanted Variation (RUV)

Normalize the dataset using RUV. All three sub-methods (RUVg, RUVs, and RUVr) can be used.

Usage

norm.RUV(raw, groups, method = c("RUVg", "RUVs", "RUVr"))

Arguments

raw: Raw read count matrix (rows = genes, cols = samples).
groups: Sample groups (subtypes)

Value

A list with the following elements:

dataNormalized: Normalized read counts.
adjustFactor: Adjusting factors for adjusting the design matrix.

list, containing dat.normed (normalized dataset), and the adjust.factor (adjusting factors) for the design matrix. The normalized dataset could only used for exploration, and adjusting factors are recommended as a covariate in the downstream analysis.

References

RUVSeq Tutorial

Examples

if (FALSE) {
  normCounts <- norm.RUV(rawCounts, groups, method="RUVg")
}