biasCorrection: Linear bias correction for microarray data

In aroneklund/bias: Visualize, Quantify, and Correct Technical Bias in Microarray Data

Description

Remove bias from an expression matrix along specified components.

Usage

  biasCorrection(x, metrics)

Arguments

x	An ExpressionSet object, or a matrix.
metrics	A data frame with bias metrics for each array.

Details

Each individual gene is fit to a multivariate linear model with metrics as the independent variables. The residuals from the fit are retained as the “bias corrected” values.

Value

Either an ExpressionSet or a matrix (corresponding to the class of x).

References

Eklund, A.C. and Szallasi, Z. (2008) Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biology, 9:R26.

See Also

getBiasMetrics

Examples

  ## For testing/example purposes only:
  ## This data set has too few samples to do meaningful bias correction
  library(affydata)
  data(Dilution)
  eset <- rma(Dilution)
  bm <- getBiasMetrics(Dilution, eset)
  esetCorrected <- biasCorrection(eset, bm)

aroneklund/bias documentation built on May 10, 2019, 1:46 p.m.