%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Do not modify this file since it was automatically generated from:
% 
%  901.Dictionary.R
% 
% by the Rdoc compiler part of the R.oo package.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\name{1. Dictionary}
\alias{1. Dictionary}
\title{1. Dictionary}


\description{
  This part describes non-obvious terms used in this package.

 \describe{
  \item{affxparser}{The name of this package.}
  \item{API}{Application program interface, which describes the
    functional interface of underlying methods.}
  \item{block}{(aka group).}
  \item{BPMAP}{A file format containing information
     related to the design of the tiling arrays.}
  \item{Calvin}{A special binary file format.}
  \item{CDF}{A file format: chip definition file.}
  \item{CEL}{A file format: cell intensity file.}
  \item{cell}{(aka feature) A probe.}
  \item{cell index}{An integer that identifies a probe uniquely.}
  \item{chip}{An array.}
  \item{chip type}{An identifier specifying a chip design
    uniquely, e.g. \code{"Mapping50K_Xba240"}.}
  \item{DAT}{A file format: contains pixel intensity
     values collected from an Affymetrix GeneArray scanner.}
  \item{feature}{A probe.}
  \item{Fusion SDK}{Open-source software development kit (SDK) provided
    by Affymetrix to access their data files.}
  \item{group}{(aka block)
    Defines a unique subset of the cells in a unit.
    Expression arrays typically only have one group per unit, whereas
    SNP arrays have either two or four groups per unit, one for each of
    the two allele times possibly repeated for both strands.}
  \item{MM}{Mismatch-match, e.g. MM probe.}
  \item{PGF}{A file format: probe group file.}
  \item{TPMAP}{A file format storing the relationship between (PM,MM)
    pairs (or PM probes) and positions on a set of sequences.}
  \item{QC}{Quality control, e.g. QC probes and QC probe sets.}
  \item{unit}{A probeset.}
  \item{XDA}{A file format, aka as the binary file format.}
 }
}
\keyword{documentation}
