getBiasMetrics2: Calculate an extended set of bias metrics

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

Description

Calculate an extended set of bias metrics from an AffyBatch object.

Usage

getBiasMetrics2(x.batch, x.rma = rma(x.batch))

Arguments

x.batch	An AffyBatch.
x.rma	An ExpressionSet calculated from x.batch.

Details

This function calculates several bias metrics for each microarray in a data set. The first four bias metrics are equivalent to those calculated by getBiasMetrics, and are those described in the publication. The other “extended” bias metrics are other numbers that might or might not be interesting.

Most of these bias metrics only make sense for Affymetrix expression arrays. Furthermore, four of the bias metrics are based on specific probes that may be missing from some Affymetrix platforms (in which case they will be NA).

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.
present.calls	The fraction of probe sets called present by mas5calls.
rma.spikes.mRNA	Mean expression value of mRNA-level control bacterial spikes.
rma.spikes.cRNA	Mean expression value of cRNA-level control bacterial spikes.
rma.rRNA	Mean expression value of five rRNA probesets.
rma.alu	Expression value of the Alu probeset.
border.plus	Median intensity of the “plus” elements of the border checkerboard (see borders).
border.minus	Median intensity of the “minus” elements of the border checkerboard (see borders).

The exact values returned here may change in future versions of this package!

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

  library(affydata)
  data(Dilution)
  bm2 <- getBiasMetrics2(Dilution)
  pairs(bm2)

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