RUVI function

RUV-I

The RUV-I algorithm. Generally used as a preprocessing step to RUV-2, RUV-4, RUV-inv, RUV-rinv, or RUVIII. RUV1 is an alias of (identical to) RUVI.

RUVI(Y, eta, ctl, include.intercept = TRUE)

RUV1(Y, eta, ctl, include.intercept = TRUE)

Arguments

• 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 opposed to sample-wise) covariates. A matrix with n columns.
• ctl: The negative controls. A logical vector of length n.
• include.intercept: Add an intercept term to eta if it does not include one already.

Details

Implements the RUV-I 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. Note that RUV1 and RUVI are two different names for the same (identical) function.

Returns

An adjusted data matrix (i.e., an adjusted Y)

References

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.

Author(s)

Johann Gagnon-Bartsch johanngb@umich.edu

See Also

RUV2, RUV4, RUVinv, RUVrinv, RUVIII