| RUV1 {ruv} | R Documentation |
The RUV-1 algorithm. Generally used as a preprocessing step to RUV-2, RUV-4, RUV-inv, or RUV-rinv.
RUV1(Y, eta, ctl)
Y |
The data. A m by n matrix, where m is the number of samples and n is the number of features. |
eta |
Gene-wise (as oposed to sample-wise) covariates. A matrix with n columns. |
ctl |
The negative controls. A logical vector of length n. |
Implements the RUV-1 algorithm as described in Gagnon-Bartsch, Jacob, and Speed (2013). Most often this algorithm is not used directly, but rather is called from RUV-2, RUV-4, RUV-inv, or RUV-rinv.
An adjusted data matrix (i.e., an adjusted Y)
Johann Gagnon-Bartsch johanngb@umich.edu
Using control genes to correct for unwanted variation in microarray data. Gagnon-Bartsch and Speed, 2012. Available at: http://biostatistics.oxfordjournals.org/content/13/3/539.full.
Removing Unwanted Variation from High Dimensional Data with Negative Controls. Gagnon-Bartsch, Jacob, and Speed, 2013. Available at: http://statistics.berkeley.edu/tech-reports/820.