2. Cell coordinates and cell indicespackage:affxparserR Documentation

_2. _C_e_l_l _c_o_o_r_d_i_n_a_t_e_s _a_n_d _c_e_l_l _i_n_d_i_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This part describes how Affymetrix _cells_, also known as _probes_
     or _features_, are address.

_C_e_l_l _c_o_o_r_d_i_n_a_t_e_s:

     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).

_C_e_l_l _i_n_d_i_c_e_s _a_n_d _c_e_l_l-_i_n_d_e_x _o_f_f_s_e_t_s:

     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.

_A_u_t_h_o_r(_s):

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

