\HeaderA{simpleaffy-deprecated}{Does simpleaffy have a QC definition file for the specified array?}{simpleaffy.Rdash.deprecated}
\aliasA{getActin3}{simpleaffy-deprecated}{getActin3}
\aliasA{getActin5}{simpleaffy-deprecated}{getActin5}
\aliasA{getActinM}{simpleaffy-deprecated}{getActinM}
\aliasA{getAllQCProbes}{simpleaffy-deprecated}{getAllQCProbes}
\aliasA{getAllSpikeProbes}{simpleaffy-deprecated}{getAllSpikeProbes}
\aliasA{getAlpha1}{simpleaffy-deprecated}{getAlpha1}
\aliasA{getAlpha2}{simpleaffy-deprecated}{getAlpha2}
\aliasA{getBioB}{simpleaffy-deprecated}{getBioB}
\aliasA{getBioC}{simpleaffy-deprecated}{getBioC}
\aliasA{getBioD}{simpleaffy-deprecated}{getBioD}
\aliasA{getCreX}{simpleaffy-deprecated}{getCreX}
\aliasA{getGapdh3}{simpleaffy-deprecated}{getGapdh3}
\aliasA{getGapdh5}{simpleaffy-deprecated}{getGapdh5}
\aliasA{getGapdhM}{simpleaffy-deprecated}{getGapdhM}
\aliasA{getTao}{simpleaffy-deprecated}{getTao}
\aliasA{haveQCParams}{simpleaffy-deprecated}{haveQCParams}
\keyword{misc}{simpleaffy-deprecated}
\begin{Description}\relax
The underlying implementation of simpleaffy has changed significantly
and it now represents QC parameters differently. In particular, it
loads only the QC data for the specified array type. A call to any of these
functions loads the appropriate environment specifed by \code{name}.
They therefore been deprecated and WILL disappear
from simpleaffy in the future.
\end{Description}
\begin{Usage}
\begin{verbatim}
  getTao(name)
  getAlpha1(name)
  getAlpha2(name)
  getActin3(name)
  getActinM(name)
  getActin5(name)
  getGapdh3(name)
  getGapdhM(name)
  getGapdh5(name)
  getAllQCProbes(name)
  getBioB(name)
  getBioC(name)
  getBioD(name)
  getCreX(name)
  getAllSpikeProbes(name)
  haveQCParams(name)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{name}] The 'clean' CDF name of the array (i.e. the result of calling
\code{\LinkA{cleancdfname}{cleancdfname}} on the \code{\LinkA{cdfName}{cdfName}}
of the AffyBatch object containing the
array data of interest.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Each of these functions has been replaced by a new function of the
form \code{qc.get.}. In order to support ratios other than gapdh and
beta-actin, the appropriate way to get ratios is now to use
\code{\LinkA{qc.get.ratios}{qc.get.ratios}}, which will return a table
containing all suggested ratio calculations for the
array.
Similarly, \code{\LinkA{qc.get.spikes}{qc.get.spikes}} will return a table
containing all spike probesets for the array.

One of the reasons for these changes is to make it easier to support
new/alternate definitions of the QC parameters for a given array.
The old functions do not know how to deal with alternate QC data
from outside the package. 

They have been left in, but deprecated - instead
the new qc.get.X() functions should be used to pick up the
additional functionality provided by, for example, the ability to use
setQCEnvironment() to specify alternate QC definition files.
\end{Details}
\begin{Value}
\end{Value}
\begin{Note}\relax
\end{Note}
\begin{Author}\relax
Crispin J Miller
\end{Author}
\begin{References}\relax
http://bioinformatics.picr.man.ac.uk/
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{setQCEnvironment}{setQCEnvironment}}
\code{\LinkA{qc}{qc}}
\code{\LinkA{qc.ok}{qc.ok}}
\code{\LinkA{cdfName}{cdfName}}
\code{\LinkA{cleancdfname}{cleancdfname}}
\code{\LinkA{qc.get.ratios}{qc.get.ratios}}
\code{\LinkA{qc.get.spikes}{qc.get.spikes}}
\code{\LinkA{qc.get.probes}{qc.get.probes}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  #old
  getBioB("hgu133plus2cdf")
  getActin3("hgu133plus2cdf")
  getActinM("hgu133plus2cdf")
  getActin5("hgu133plus2cdf")
  #new
  setQCEnvironment("hgu133plus2cdf")
  qc.get.spikes()["bioB"]
  r <- qc.get.probes()
  r["actin3"]
  r["actinM"]
  r["actin5"]
\end{ExampleCode}
\end{Examples}