marrayLayout-class          package:marray          R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_L_a_y_o_u_t", _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _l_a_y_o_u_t _p_a_r_a_m_e_t_e_r_s _o_f _c_D_N_A _m_i_c_r_o_a_r_r_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class is used to keep track of important layout parameters
     for two-color cDNA microarrays. It contains slots for: the total
     number of spotted probe sequences on the array, the dimensions of
     the spot and grid matrices, the plate origin of the probes,
     information on spotted control sequences (e.g. probe sequences
     which should have equal abundance in the two target samples, such
     as housekeeping genes). The terms _print-tip-group_, _grid_, _spot
     matrix_, and _sector_ are used interchangeably and refer to a set
     of spots printed using the same print-tip.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form ' 
     new('marrayLayout','
      '    maNgr      = ...., # Object of class numeric'
      '    maNgc      = ...., # Object of class numeric'
      '    maNsr      = ...., # Object of class numeric'
      '    maNsc      = ...., # Object of class numeric'
      '    maNspots   = ...., # Object of class numeric'
      '    maSub      = ...., # Object of class logical'
      '    maPlate    = ...., # Object of class factor'
      '    maControls = ...., # Object of class factor'
      '    maNotes    = ...., # Object of class character'
      '  )'

_S_l_o_t_s:

     '_m_a_N_g_r': Object of class '"numeric"', number of rows for the grid
          matrix.

     '_m_a_N_g_c': Object of class '"numeric"', number of columns for the
          grid matrix.

     '_m_a_N_s_r': Object of class '"numeric"', number of rows for the spot
          matrices.

     '_m_a_N_s_c': Object of class '"numeric"', number of columns for the
          spot matrices.

     '_m_a_N_s_p_o_t_s': Object of class '"numeric"', total number of spots on
          the array, equal to maNgr x maNgc x maNsr x maNsc.

     '_m_a_S_u_b': Object of class '"logical"',  indicating which spots are
          currently being considered.

     '_m_a_P_l_a_t_e': Object of class '"factor"', recording the plate origin
          of the spotted probe sequences.

     '_m_a_C_o_n_t_r_o_l_s': Object of class '"factor"', recording the control
          status of the spotted probe sequences.

     '_m_a_N_o_t_e_s': Object of class '"character"', any notes concerning the
          microarray layout, e.g., printing conditions.

_M_e_t_h_o_d_s:

     [ 'signature(x = "marrayLayout")': subsetting operator for spots
          on the array, ensures that all slots are subset properly.

     _m_a_C_o_n_t_r_o_l_s<- 'signature(object = "marrayLayout")': slot assignment
          method. 

     _m_a_C_o_n_t_r_o_l_s 'signature(object = "marrayLayout")': slot accessor
          method.

     _m_a_G_r_i_d_C_o_l 'signature(object = "marrayLayout")': method which
          computes a vector of grid column coordinates for each spot.

     _m_a_G_r_i_d_R_o_w 'signature(object = "marrayLayout")': method which
          computes a vector of grid row coordinates for each spot.

     _m_a_L_a_y_o_u_t<- 'signature(object = "marrayRaw", value =
          "marrayLayout")': slot assignment method. 

     _m_a_L_a_y_o_u_t<- 'signature(object = "marrayNorm", value =
          "marrayLayout")': slot assignment method. 

     _m_a_N_g_c 'signature(object = "marrayLayout")': slot accessor method.

     _m_a_N_g_c<- 'signature(object = "marrayLayout", value = "numeric")':
          slot assignment method.

     _m_a_N_g_r 'signature(object = "marrayLayout")': slot accessor method.

     _m_a_N_g_r<- 'signature(object = "marrayLayout", value = "numeric")':
          slot assignment method.

     _m_a_N_o_t_e_s 'signature(object = "marrayLayout")': slot accessor
          method.

     _m_a_N_o_t_e_s<- 'signature(object = "marrayLayout", value =
          "character")': slot assignment method. 

     _m_a_N_s_c 'signature(object = "marrayLayout")': slot accessor method.

     _m_a_N_s_c<- 'signature(object = "marrayLayout", value = "numeric")':
          slot assignment method.

     _m_a_N_s_p_o_t_s 'signature(object = "marrayLayout")': slot accessor
          method.

     _m_a_N_s_p_o_t_s<- 'signature(object = "marrayLayout", value =
          "numeric")': slot assignment method.

     _m_a_N_s_r 'signature(object = "marrayLayout")': slot accessor method.

     _m_a_N_s_r<- 'signature(object = "marrayLayout", value = "numeric")':
          slot assignment method.

     _m_a_P_l_a_t_e 'signature(object = "marrayLayout")': slot accessor
          method.

     _m_a_P_l_a_t_e<- 'signature(object = "marrayLayout")': slot assignment
          method. 

     _m_a_P_r_i_n_t_T_i_p 'signature(object = "marrayLayout")': method which
          computes a vector of print-tip-group indices for each spot.

     _m_a_S_p_o_t_C_o_l 'signature(object = "marrayLayout")': method which
          computes a vector of spot column coordinates for each spot.

     _m_a_S_p_o_t_R_o_w 'signature(object = "marrayLayout")': method which
          computes a vector of spot row coordinates for each spot.

     _m_a_S_u_b 'signature(object = "marrayLayout")': slot accessor method.

     _m_a_S_u_b<- 'signature(object = "marrayLayout", value = "logical")':
          slot assignment method. 

     _m_a_S_u_b<- 'signature(object = "marrayLayout", value = "numeric")':
          slot assignment method. 

     _p_r_i_n_t 'signature(x = "marrayLayout")': print method for
          '"marrayLayout"' class.

_A_u_t_h_o_r(_s):

     Sandrine Dudoit, <URL: http://www.stat.berkeley.edu/~sandrine>.

_R_e_f_e_r_e_n_c_e_s:

     S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for
     exploratory analysis and normalization of cDNA microarray data. In
     G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger,
     editors, _The Analysis of Gene Expression Data: Methods and
     Software_, Springer, New York.

_S_e_e _A_l_s_o:

     'marrayRaw', 'marrayNorm', 'marrayInfo' and '[-methods'.

_E_x_a_m_p_l_e_s:

     ## See marrayRaw