\name{YAQCStats-class}
\docType{class}
\alias{YAQCStats-class}


\alias{isLog,YAQCStats-method}
\alias{target,YAQCStats-method}
\alias{avns,YAQCStats-method}
\alias{moreSpikeInProbes,YAQCStats-method}
\alias{gcosProbes,YAQCStats-method}
\alias{bioCalls,YAQCStats-method}
\alias{objectVersion,YAQCStats-method}
\alias{getYaqcControlProbes,YAQCStats-method}

\alias{isLog-methods}
\alias{target-methods}
\alias{avns-methods}
\alias{moreSpikeInProbes-methods}
\alias{gcosProbes-methods}
\alias{bioCalls-methods}
\alias{arrays-methods}
\alias{objectVersion,method}
\alias{getYaqcControlProbes,method}

\alias{plot,YAQCStats,ANY-method}
\alias{summary,YAQCStats,ANY-method}
\alias{show,YAQCStats-method}
\alias{merge,YAQCStats-method}
\alias{arrays,YAQCStats-method}

\title{Class "YAQCStats" }
\description{Holds Quality Control Data for a set of Affymetrix Arrays}
\section{Objects from the Class}{
    Objects can be created by calls of the form \code{yaqc(object)}
    where object is of class \code{AffyBatch} of \code{ExpressionSet}.
    YAQCStats is a subclass of \code{QCStats} and uses the
    \code{scale.factor}, \code{average.background} and
    \code{percent.present}, \code{arraytype} and \code{target}
    attributes of it's super-class. 
}
\section{Slots}{
  \describe{
    \item{\code{log}:}{Object of class \code{"logical"} that
      specifies if expression values are in log2 form.}
    \item{\code{average.noise}:}{Object of class \code{"numeric"}.
      The average noise for the arrays.}
    \item{\code{morespikes}:}{Object of class \code{"matrix"}.
      More spiked in probes (e.g. r2biob5, r2biob3,...).}
    \item{\code{gcos.probes}:}{Object of class \code{"matrix"}.
      GAPDH and \eqn{\beta}-actin qc probes 
      (e.g. gapdh 3,5,M,...) containing the GCOS values.}
    \item{\code{bio.calls}:}{Object of class \code{"matrix"}.
      BioB 5',3',M and BioC, BioC 5',3' 
      present/absent/marginal calls .}
    \item{\code{objectVersion}}{Character describing the version
      of the library used to generate the \code{YAQCStats} object.}
    \item{\code{yaqcControlProbes}}{Object of class \code{YaqcControlProbes}
      that defines the different probes used for the quality
      control.}
  }
}

\section{Methods}{
  \describe{
    \item{isLog}{\code{signature(object = "YAQCStats")}: are intensities
      in log2 form.}
    \item{avns}{\code{signature(object = "YAQCStats")}: average noise.}
    \item{moreSpikeInProbes}{\code{signature(object = "YAQCStats")}:
      more spike-in probes.}
    \item{gcosProbes}{\code{signature(object = "YAQCStats")}: GCOS
      values of gapdh and actin QC probes.}
    \item{bioCalls}{\code{signature(object = "YAQCStats")}: P/M/A calls
      for BioB, BioC and BioD spikes.}
   \item{arrays}{\code{signature(object = "YAQCStats")}: shows the array
     names composing the \code{YAQCStats} object.}
    \item{plot}{\code{signature(object = "YAQCStats")}: visual
  representation of the qc metrics.}
    \item{summary}{\code{signature(object = "YAQCStats")}: data frame
      summary of the outliers.}
    \item{show}{\code{signature(object = "YAQCStats")}: displays the content
      of the object as a data frame.} 
    \item{merge}{\code{signature(object = "YAQCStats")}: merges two
      compatible YAQCStats objects, i.e. that have the same values for the
      \code{log}, \code{target} and \code{arraytype} slots.}
    \item{arrays}{\code{signature(object = "YAQCStats")}: shows the array
      names of an YAQCStats objects. }
    \item{objectVersion}{\code{signature(object = "YAQCStats")}: shows
      the library verison used to generate the \code{YAQCStats} object.}
    \item{getYaqcControlProbes}{\code{signature(object = "YAQCStats")}:
      returns the \code{YaqcControlProbes} object that has been used to
      generate the current \code{YAQCStats} object.}
  }
}

\author{ Laurent Gatto }

\seealso{QCStats-class,YaqcControlProbes-class}

\keyword{classes}