PrintLayout              package:limma              R Documentation

_P_r_i_n_t _L_a_y_o_u_t - _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A list-based class for storing information about the process used
     to print spots on a microarray.

     'PrintLayout' objects can be created using 'getLayout'. The
     'printer' component of an 'RGList' or 'MAList' object is of this
     class.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects of this class contains no slots but should contain the
     following list components:

       'ngrid.r':  number of grid rows on the arrays
       'ngrid.c':  number of grid columns on the arrays
       'nspot.r':  number of rows of spots in each grid
       'nspot.c':  number of columns of spots in each grid
       'ndups':    number of duplicates of each DNA clone, i.e., number of times print-head dips into each well of DNA
       'spacing':  number of spots between duplicate spots.  Only applicable if 'ndups>1'. 'spacing=1' for side-by-side spots by rows, 'spacing=nspot.c' for side-by-side spots by columns, 'spacing=ngrid.r*ngrid.c*nspot.r*nspot.c/2' for duplicate spots in top and bottom halves of each array.
       '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.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     2.Classes gives an overview of all the classes defined by this
     package.

_E_x_a_m_p_l_e_s:

     #  Settings for Swirl and ApoAI example data sets in User's Guide

     printer <- list(ngrid.r=4, ngrid.c=4, nspot.r=22, nspot.c=24, ndups=1, spacing=1, npins=16, start="topleft")

     #  Typical settings at the Australian Genome Research Facility

     #  Full pin set, duplicates side-by-side on same row
     printer <- list(ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20, ndups=2, spacing=1, npins=48, start="topright")

     #  Half pin set, duplicates in top and lower half of slide
     printer <- list(ngrid.r=12, ngrid.c=4, nspot.r=20, nspot.c=20, ndups=2, spacing=9600, npins=24, start="topright")

