RUVSeq (version 1.6.2)

RUVSeq-package: Remove Unwanted Variation from RNA-Seq Data

Description

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.

References

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).

See Also

RUVg, RUVr, RUVs