This package implements the remove unwanted variation (RUV) methods of
Risso et al. (2014) for the normalization of RNA-Seq read counts between
samples.
Details
Package:
RUVSeq
Type:
Package
Version:
0.99.1
Date:
2014-04-15
License:
Artistic-2.0
The RUVg function implements the RUVg normalization
procedure of Risso et al. (2014), by using control genes to remove
unwanted variation from the RNA-Seq read counts.
See also RUVr and RUVs for the "residual"
and "sample" methods, based, respectively, on residuals (e.g., deviance
residuals from a first-pass GLM regression of the unnormalized counts
on the covariates of interest) and replicate/negative control
samples for which the covariates of interest are constant.
D. Risso, J. Ngai, T. P. Speed, and S. Dudoit.
Normalization of RNA-seq data using factor analysis of control genes or samples.
Nature Biotechnology, 2014. (In press).
D. Risso, J. Ngai, T. P. Speed, and S. Dudoit. The role of spike-in
standards in the normalization of RNA-Seq. In D. Nettleton and S. Datta,
editors, Statistical Analysis of Next Generation Sequence
Data. Springer, 2014. (In press).