cellxy {affxparser}R Documentation

Cell coordinates and cell indices

Description

This part describes how Affymetrix cells, also known as probes or features, are address.

Cell coordinates

In Affymetrix data files, cells are uniquely identified by there cell coordinates, i.e. (x,y). For an array with N*K cells in N rows and K columns, the x coordinate is an integer in [0,K-1], and the y coordinate is an integer in [0,N-1]. The cell in the upper-left corner has coordinate (x,y)=(0,0) and the one in the lower-right corner (x,y)=(K-1,N-1).

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 cell index, i, of cell (x,y) as

i = K*y + x + 1,

where one is added to give indices in [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 (N,K)=(1600,1600) the cell at (x,y)=(0,0) has index i=1, and the cell at (x,y)=(1599,1599) has index i=2600000.

Given the cell index i, the coordinate (x,y) can be calculated as

y = mod(i-1, K)

x = (i-1)-K*y.

Continuing the above example, the coordinate for cell i=1 is thus (x,y)=(0,0) and for cell i=2600000 it is (x,y)=(1599,1599).

Although not needed to use the methods in this package, to get the cell indices for the cell coordinates or vice versa, see xy2indices and indices2xy() in the affy package.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package affxparser version 1.4.1 Index]