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ruv (version 0.9.7.1)

RUVI: RUV-I

Description

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.

Usage

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.

Value

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

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.

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.

See Also

RUV2, RUV4, RUVinv, RUVrinv, RUVIII