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)

_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

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

     A 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)

