RUV -- Remove Unwanted Variation

R packages

ruv

The ruv package implements RUV-2, RUV-4, RUV-inv, RUV-rinv, and various supporting methods. It is available on CRAN at:

ruv (version: 0.9.4)

ruv.extras

The ruv.extras package provides functions for generating diagnostic plots, along with example scripts that run differential expression analyses and format the output nicely in the form of a web page. An example is here and a how-to is here.

The example code provided in the ruv.extras package may change considerably in future releases, and it is not recommended that you create any packages (or other "permanent" code) that depend on it. For this reason the ruv.extras package is not on CRAN, but is instead available below. Note that ruv.extras depends on ruv.htmllatex, also available below.

ruv.extras (0.9.4)
ruv.htmllatex (0.9.4)

Data Packages

The data packages below provide the datasets used by Gagnon-Bartsch and Speed (2012) and Gagnon-Bartsch, Jacob and Speed (2013).

ruv.data.gender.sm
ruv.data.gender.bgnmsm
ruv.data.gender.bgnmsmls
ruv.data.alzheimers.sm
ruv.data.alzheimers.bgnmsm

How To

This how-to is meant to help you get started with the ruv.extras package.

How To

References

Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch, J.A. and Speed, T.P. Biostatistics. 2012.

Removing Unwanted Variation from High Dimensional Data with Negative Controls. Gagnon-Bartsch, J.A., Jacob, L. and Speed, T.P. Tech Report.

Additional Resources

This is a list of the housekeeping genes used in the analyses. The list is taken from Eisenberg and Levanon (2003).

Other resources (including code) may be available upon request. Please feel free to contact me.