getBiasMetrics: Calculate bias metrics

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

Description

Calculate bias metrics from an AffyBatch object. These are the original four bias metrics as described in the Genome Biology article.

Usage

  getBiasMetrics(x.batch, x.rma = rma(x.batch))

Arguments

x.batch	An AffyBatch.
x.rma	An ExpressionSet calculated from x.batch (optional).

Details

This function calculates four bias metrics for each microarray in a data set.

Three of the bias metrics are derived from the raw intensities in x.batch and one is derived from the probeset-summarized expression values in x.rma. If x.rma is missing, the expression values will be computed using rma.

Value

A data frame containing bias metrics for each array.

pm.median	Median intensity of all perfect-match probes on the array.
pm.IQR	Interquartile range of all perfect-match probes on the array.
rma.IQR	Interquartile range of all expression values on the array.
degradation	The slope returned by AffyRNAdeg; indicates the relative preference for 3'-biased probes in a probe set.

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

biasCorrection; also qc in the simpleaffy package.

Examples

  library(affydata)
  data(Dilution)
  bm <- getBiasMetrics(Dilution)
  pairs(bm)

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