printorder               package:limma               R Documentation

_I_d_e_n_t_i_f_y _O_r_d_e_r _i_n _w_h_i_c_h _S_p_o_t_s _w_e_r_e _P_r_i_n_t_e_d

_D_e_s_c_r_i_p_t_i_o_n:

     Identify order in which spots were printed and the 384-well plate
     from which they were printed.

_U_s_a_g_e:

     printorder(layout, ndups=1, spacing="columns", npins, start="topleft")

_A_r_g_u_m_e_n_t_s:

  layout: list with the components 'ngrid.r', 'ngrid.c', 'nspot.r' and
          'nspot.c', or an 'RGList' or 'MAList' object from which the
          printer layout may be extracted.

   ndups: number of duplicate spots, i.e., number of times print-head
          dips into each well

 spacing: character string indicating layout of duplicate spots.
          Choices are '"columns"', '"rows"' or '"topbottom"'.

   npins: actual number of pins or tips on the print-head

   start: character string giving position of the spot printed first in
          each grid. Choices are '"topleft"' or '"topright"' and
          partial matches are accepted.

_D_e_t_a_i_l_s:

     In most cases the printer-head contains the 'layout$ngrid.r' times
     'layout$ngrid.c' pins or tips and the array is printed using
     'layout$nspot.r' times 'layout$npot.c' dips of the head. The plate
     holding the DNA to be printed is assumed to have 384 wells in 16
     rows and 24 columns.

     'ndups' indicates the number of spots printed from each well. The
     replicate spots from multiple dips into the same wells are assumed
     to be side-by-side by columns ('spacing="columns"'), by rows
     ('spacing="rows"') or in the top and bottom halves of the array
     ('spacing="topbottom"').

     In some cases a smaller number of physical pins is used and the
     total number of grids is built up by effectively printing two or
     more sub-arrays on the same slide. In this case the number of
     grids should be a multiple of the number of pins.

     Printing is assumed to proceed by rows within in each grid
     starting either from the top-left or the top-right.

_V_a_l_u_e:

     List with components 

printorder: numeric vector giving printorder of each spot, i.e., which
          dip of the print-head was used to print it

   plate: numeric vector giving plate number from which each spot was
          printed

 plate.r: numeric vector giving plate-row number of the well from which
          each spot was printed

 plate.c: numeric vector giving plate-column number of the well from
          which each spot was printed

plateposition: character vector summarizing plate number and plate
          position of the well from which each spot was printed with
          letters for plate rows and number for columns. For example
          '02B13' is second row, 13th column, of the second plate.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'normalizeForPrintorder'.

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

_E_x_a_m_p_l_e_s:

     printorder(list(ngrid.r=2,ngrid.c=2,nspot.r=12,nspot.c=8))

