naiveReplicateRUV
(Package: RUVnormalize) :
Remove unwanted variation from a gene expression matrix using replicate samples
The function takes as input a gene expression matrix as well as the index of negative control genes and replicate samples. It estimates and remove unwanted variation from the gene expression.
clScore
(Package: RUVnormalize) :
Computes a distance between two partitions of the same data
The function takes as input two partitions of a dataset into clusters, and returns a number which is small if the two partitions are close, large otherwise.
The function takes as input a gene expression matrix as well as the index of negative control genes and replicate samples. It estimates and remove unwanted variation from the gene expression. The major difference with naiveRandRUV and naiveReplicateRUV is that iterativeRUV jointly estimates the factor of interest and the unwanted variation term. It does so iteratively, by estimating each term using the current estimate of the other one.
naiveRandRUV
(Package: RUVnormalize) :
Remove unwanted variation from a gene expression matrix using negative control genes
The function takes as input a gene expression matrix as well as the index of negative control genes. It estimates unwanted variation from these control genes, and removes them by regression, using ridge and/or rank regularization.
providing 
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