borders: Get border intensity values from an AffyBatch object

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

Description

Get border intensity values from an AffyBatch object

Usage

borders(x.batch)

Arguments

x.batch

An AffyBatch object.

Details

The borders of Affy arrays form a plus/minus checkerboard; this function returns their intensities.

Value

A list of lists:

plus	A list of four vectors, containing the bottom, left, top, and right “plus” values.
minus	A list of four vectors, containing the bottom, left, top, and right “minus” values.

See Also

The package affyQCReport.

Examples

  

  library(affydata)
  data(Dilution)
  
  bord <- borders(Dilution)

  bord.all <- sapply(bord, unlist)

  plotDensity(log2(bord.all),
    xlab = 'log2 intensity',
    main = 'Array border intensity distribution')
  legend('topright', legend = sampleNames(Dilution),
    lty = 1:4, col = 1:4)

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