yaqcaffy (version 1.32.0)

yaqc.plot: Plots a YAQCStats object

Description

S4 method to plot an YAQCStats object. plot(object) generates a visual summary of the various Affymetrix QC statistics.

Usage

yaqc.plot(YAQCStatsObject, which=c("all","sfs","avbg","avns","pp","gapdh","actin","bio","spikes"), ...)

Arguments

YAQCStatsObject

An object of class YAQCStats.

which

Which quality metrics should be plotted (all by default). See below for details.

...

Other arguments passed to the respective plot methods.

Details

The quality control metrics of the YAQCStatsObject are plotted in a serie of graphs with the recommended ranges.

The scale factors are represented through a dot chart and the upper and lower limits are defined with vertical red lines. The other qc metircs are shown using dot plots. For the upper row box plots (average background, average noise, percent present and $\beta$-actin and GAPDH ratios, the mean is represented by a dashed red line and the mean +/- 2 stdev by red dotted lines. For the lower box plots, featuring the internal controls, grey boxes defines the mean (middle segment) +/- 2 stdev.

Individual plots can also be generated with the which argument: 'sfs' for the scale factor, 'avbg' and 'avns' for the average background and noise, 'pp' for the percentage of present calls, 'gapdh' and 'actin' for the GAPDH and $\beta$-actin ratios, 'bio' for the hybridization controls and 'spikes' for the retro-transciption spiked controls.

If the YAQCStatsObject has been generated with an Expression Set objects, the scale factors, average noise and background and percent present can not be computed and the respective plots are removed from the final graph.

Examples

  ## load data
  library(affydata)
  data(Dilution)
  ## create the yaqc object
  ## and plot it
  qobj <- yaqc(Dilution)
  plot(qobj)