This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.
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.
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.
Davide Risso and Sandrine Dudoit
Maintainer: Davide Risso <email@example.com>
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).
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