\name{plot.qc.stats}
\alias{plot.qc.stats}
\alias{plot,QCStats}
\alias{plot,QCStats,missing-method}

\title{ Plots a QCStats object }
\description{
  Generates a visual summary of the various QC statistics recommended by Affymetrix in their 'Data Analysis Fundamentals' handbook.
}
\section{Usage}{
plot.qc.stats(x, fc.line.col = "black", sf.ok.region = "light blue", chip.label.col = "black", sf.thresh = 3, gdh.thresh = 1.25, ba.thresh = 3, present.thresh = 10, bg.thresh = 20, label = NULL,title="QC Stats",spread=c(-8,8),usemid=F,type="l",cex=1, ...)
}
\arguments{
  \item{x}{ A \code{QCStats} object }
  \item{fc.line.col}{ The colour to mark fold change lines with }
  \item{sf.ok.region}{ The colour to mark the region in which scale factors lie within appropriate bounds }
  \item{chip.label.col}{ The colour to label the chips with }
  \item{sf.thresh}{ Scale factors must be within this fold-range }
  \item{gdh.thresh}{ Gapdh ratios must be within this range }
  \item{ba.thresh}{ beta actin must be within this range }
  \item{present.thresh}{ The percentage of genes called present must lie within this range }
  \item{bg.thresh}{ Array backgrounds must lie within this range }
  \item{label}{ What to call the chips }
  \item{main}{ The title for the plot }
  \item{usemid}{ If true use 3'/M ratios for the GAPDH and beta actin probes }
  \item{cex}{ Value to scale character size by (e.g. 0.5 means that the text should be plotted half size) }
  \item{\dots}{ Other parameters to pass through to \code{plot} }
}
\details{

A lot of information is presented in this one figure. By default,
each array is represented by a seperate line in the figure. The
central vertical line corresponds to 0 fold change, the dotted lines
on either side correspond to 3 fold up and down regulation. The blue
bar represents the region in which all arrays have scale factors
within, by default, three-fold of each other. Its position is found by
calculating the mean scale factor for all chips and placing the center
of the region such that the borders are -1.5 fold up or down from the
mean value.

Each array is plotted as a line from the 0-fold line to the point
that corresponds to its scale factor. If the ends of all of the lines
are in the blue region, their scale-factors are compatible. The lines
are coloured blue if OK, red if not.

The figure also shows GAPDH and beta-actin 3'/5' ratios. These are
represented as a pair of points for each chip. Affy state that beta
actin should be within 3, gapdh around 1. Any that fall outside these
thresholds (1.25 for gapdh) are coloured red; the rest are blue.

Written along the left hand side of the figure are the number of genes called
present on each array and the average background. These will vary
according to the samples being processed, and Affy's QC suggests
simply that they should be similar. If any chips have significantly
different values this is flagged in red, otherwise the numbers are
displayed in blue. By default, 'significant' means that \%-present are
within 10\% of each other; background intensity, 20 units. These last
numbers are somewhat arbitrary and may need some tweaking to find
values that suit the samples you're dealing with, and the overall
nature of your setup.

Finally, if BioB is not present on a chip, this will be flagged by
printing 'BioB' in red.

In short, everything in the figure should be blue - red highlights a problem!

}
\author{ Crispin J Miller }

\seealso{ \code{\link[simpleaffy]{qc}} }
\examples{
  data(qcs)
  plot(qcs)
}


\keyword{ misc }