```
#########################################################################/**
# @RdocDocumentation "2. Cell coordinates and cell indices"
#
# \description{
# This part describes how Affymetrix \emph{cells}, also known as
# \emph{probes} or \emph{features}, are addressed.
# }
#
# \section{Cell coordinates}{
# In Affymetrix data files, cells are uniquely identified by there
# \emph{cell coordinates}, i.e. \eqn{(x,y)}. For an array with
# \eqn{N*K} cells in \eqn{N} rows and \eqn{K} columns, the \eqn{x}
# coordinate is an integer in \eqn{[0,K-1]}, and the \eqn{y} coordinate
# is an integer in \eqn{[0,N-1]}. The cell in the upper-left corner has
# coordinate \eqn{(x,y)=(0,0)} and the one in the lower-right corner
# \eqn{(x,y)=(K-1,N-1)}.
# }
#
# \section{Cell indices and cell-index offsets}{
# To simplify addressing of cells, a coordinate-to-index function is
# used so that each cell can be addressed using a single integer instead
# (of two). Affymetrix defines the \emph{cell index}, \eqn{i}, of
# cell \eqn{(x,y)} as
# \deqn{
# i = K*y + x + 1,
# }
# where one is added to give indices in \eqn{[1,N*K]}.
# Continuing, the above definition means that cells are ordered
# row by row, that is from left to right and from top to bottom,
# starting at the upper-left corner.
# For example, with a chip layout \eqn{(N,K)=(1600,1600)} the cell at
# \eqn{(x,y)=(0,0)} has index i=1, and the cell at \eqn{(x,y)=(1599,1599)}
# has index \eqn{i=2560000}.
# A cell at \eqn{(x,y)=(1498,3)} has index \eqn{i=6299}.
#
# Given the cell index \eqn{i}, the coordinate \eqn{(x,y)} can be
# calculated as
# \deqn{
# y = floor((i-1)/K)
# }
# \deqn{
# x = (i-1)-K*y.
# }
# Continuing the above example, the coordinate for cell \eqn{i=1} is
# be found to be \eqn{(x,y)=(0,0)}, for cell \eqn{i=2560000} it is
# \eqn{(x,y)=(1599,1599)}, for cell \eqn{i=6299} is it
# \eqn{(x,y)=(1498,3)}.
# }
#
# \section{Converting between cell indices and (x,y) coordinates in R}{
# Although not needed to use the methods in this package, to get the
# cell indices for the cell coordinates or vice versa, see
# \code{\link[affy:xy2indices]{xy2indices}()} and \code{indices2xy()}
# in the \bold{affy} package.
# }
#
# \section{Note on the zero-based "index" field of Affymetrix CDF files}{
# An Affymetrix CDF file provides information on which cells should be
# grouped together. To identify these groups of cells, the cells
# are specified by their (x,y) coordinates, which are stored as
# zero-based coordinates in the CDF file.
#
# All methods of the \pkg{affxparser} package make use of these
# (x,y) coordinates, and some methods make it possible to read
# them as well. However, it is much more common that the methods
# return cell indices \emph{calculated} from the (x,y) coordinates
# as explained above.
#
# In order to conveniently work with cell indices in \R, the
# convention in \emph{affxparser} is to use \emph{one-based}
# indices.
# Hence the addition (and subtraction) of 1:s in the above equations.
# This is all taken care of by \pkg{affxparser}.
#
# Note that, in addition to (x,y) coordinates, a CDF file also contains
# a one-based "index" for each cell. This "index" is redundant to
# the (x,y) coordinate and can be calculated analogously to the
# above \emph{cell index} while leaving out the addition (subtraction)
# of 1:s.
# Importantly, since this "index" is redundant (and exists only in
# CDF files), we have decided to treat this field as an internal field.
# Methods of \pkg{affxparser} do neither provide access to nor make
# use of this internal field.
# }
#
# @author "HB"
##*/#########################################################################
```

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