Normalization By Surrogate Variable Analysis for Sequencing Data (SVA)

Normalize the dataset using SVA, and return the normalized dataset with adjusting factor.

norm.SVA(raw, groups)

Arguments

raw	raw count data in the format of data frame or matrix, with columns for samples and rows for genes.
groups	vector of characters indicating the group for each sample.
calibrator	whether the raw dataset includes the known negative control genes which should contain "cali" in the gene names.

Value

list, containing dat.normed (normalized dataset) without the calibrators, and the adjust.factor (adjusting factors) for the design matrix. The normalized dataset could only used for exploration.

References

SVA Package

Examples

test.SVA <- norm.SVA(data.test, data.group)