getLayout               package:limma               R Documentation

_E_x_t_r_a_c_t _t_h_e _P_r_i_n_t _L_a_y_o_u_t _o_f _a_n _A_r_r_a_y _f_r_o_m _t_h_e _G_A_L _F_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     From the Block, Row and Column information in the GAL file,
     determine the number of grid rows and columns on the array and the
     number of spot rows and columns within each grid.

_U_s_a_g_e:

     getLayout(gal, guessdups=FALSE)

_A_r_g_u_m_e_n_t_s:

     gal: data.frame containing the GAL, i.e., giving the position and
          gene identifier of each spot

guessdups: logical, if 'TRUE' then try to determine number and spacing
          of duplicate spots, i.e., within-array replicates

_D_e_t_a_i_l_s:

     A Gene Allocation List (GAL) file is a list of genes and
     associated information produced by an Axon microarray scanner.
     This function assumes that the data.frame contains columns
     'Block', 'Column' and 'Row'. The number of tip columns is not
     determinable from the GAL but is assumed to be four.

_V_a_l_u_e:

     A list with components 

 ngrid.r: integer, number of grid rows on the arrays

 ngrid.c: integer, number of grid columns on the arrays

 nspot.r: integer, number of rows of spots in each grid

 nspot.c: integer, number of columns of spots in each grid

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'gpTools'.

     An overview of LIMMA functions for reading data is given in
     3.ReadingData.

_E_x_a_m_p_l_e_s:

     # gal <- readGAL()
     # layout <- getLayout(gal)

