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 a genelist,
     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)
     getLayout2(galfile)

_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

 galfile: name or path of GAL file

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 GenePix Array List (GAL) file is a list of genes and associated
     information produced by an Axon microarray scanner. The function
     'getLayout' determines the print layout from a data frame created
     from a GAL file or gene list. The data.frame must contain columns
     'Block', 'Column' and 'Row'. (The number of tip columns is not
     assumed to be either one or four.) The function 'getLayout2'
     determines the print layout from the header information of an
     actual GAL file.

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

     A 'printlayout' object, which is a list with the following
     components. The last two components are present only if
     'guessdups=TRUE'. 

 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

   ndups: integer, number of times each probe is printed on the array

 spacing: integer, spacing between multiple printings of each probe

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

     Gordon Smyth and James Wettenhall

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

     'gpTools'.

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

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

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

