R: RUV-1

RUV1 {ruv} | R Documentation

## RUV-1

### Description

The RUV-1 algorithm. Generally used as a preprocessing step to RUV-2, RUV-4, RUV-inv, or RUV-rinv.

### Usage

    RUV1(Y, eta, ctl)

### 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 oposed to sample-wise) covariates. A matrix with n columns.
`ctl` | The negative controls. A logical vector of length n.

### Details

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.

### Value

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

### Author(s)

Johann Gagnon-Bartsch johanngb@umich.edu

### 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`

[Package ruv version 0.9.6 Index]