S4 method to plot an
plot(object) generates a visual summary of the various Affymetrix QC statistics.
An object of class
Which quality metrics should be plotted (all by default). See below for details.
Other arguments passed to the respective
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 β-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
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 β-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.
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