Assessments of normalization performance

Usage

AssessNormalization(
  data.ls,
  bio.group = NULL,
  enrich.group = NULL,
  batch.group = NULL,
  eval.pam.k = 2:6,
  eval.pc.n = 3,
  log = TRUE,
  pos.eval.set = NULL,
  neg.eval.set = NULL
)

Arguments

data.ls: List containing normalized counts and adjust factors for adjusting unwanted variation. Output of ApplyNormalization.
bio.group: Vector of index indicating the column index of samples of each biological groups in the raw/normalized count data matrix.
enrich.group: Vector of index indicating the column index of enrichment and input samples in the raw/normalized count data matrix.
batch.group: Vector of index indicating the column index of each batch groups in the raw/normalized count data matrix.
eval.pam.k: Integer or vector of integers indicates the number of clusters for PAM clustering in performance evaluation, default: 2:6.
eval.pc.n: Integer indicates the evaluation metrics will be calculated in the first nth PCs, default: 3.
log: Whether to perform log2-transformation with 1 offset on data matrix, default: TRUE.
pos.eval.set: Vector of genes id.
neg.eval.set: Vector of genes id.

Value

List containing the metrics matrix and the ranking matrix, both sorted by the score of methods from top to bottom.