RUV -- Remove Unwanted Variation
ruvThe ruv package implements RUV-2, RUV-4, RUV-inv, RUV-rinv, and various supporting methods. It is available on CRAN at:
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.
Data PackagesThe data packages below provide the datasets used by Gagnon-Bartsch and Speed (2012) and Gagnon-Bartsch, Jacob and Speed (2013).
How ToThis how-to is meant to help you get started with the ruv.extras package.
ReferencesUsing 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 ResourcesThis 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.