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)
     getDupSpacing(ID)

_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

      ID: vector or factor of gene IDs

_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 assumed
     to be either one or four.)

     On some arrays, each probe may be duplicated a number of times
     ('ndups') at regular intervals ('spacing') in the GAL file.
     'getDupSpacing' determines valid values for 'ndups' and 'spacing'
     from a vector of IDs. If 'guessdups=TRUE', then 'getLayout' calls
     'getDupSpacing'.

     The function 'getLayout2' attempts to determine 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)