marrayTwo-class        package:marrayClasses        R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_T_w_o", _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _m_i_c_r_o_a_r_r_a_y _s_p_o_t _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class represents pre- or post-normalization intensity data
     for a batch of cDNA microarrays. A _batch of arrays_ consists of a
     collection of arrays with the same layout  ('"marrayLayout"'). The
     class contains slots for two types of spot statistics (e.g. the
     raw green (Cy3) and red (Cy5) foreground  intensities, or
     normalized log-ratios M and average intensities A), the layout of
     the arrays, and a description of the target samples hybridized to
     the arrays

_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('marrayRaw','
      '    maX      = ...., # Object of class matrix'
      '    maY      = ...., # Object of class matrix'
      '    maLayout  = ...., # Object of class marrayLayout'
      '    maTargets = ...., # Object of class marrayInfo'
      '  )'

_S_l_o_t_s:

     '_m_a_X': Object of class '"matrix"', any spot statistic, rows
          correspond to spotted probe sequences, columns to arrays in
          the batch.

     '_m_a_Y': Object of class '"matrix"', any spot statistic, rows
          correspond to spotted probe sequences, columns to arrays in
          the batch.

     '_m_a_L_a_y_o_u_t': Object of class '"marrayLayout"',  layout parameters
          for the cDNA microarrays.

     '_m_a_T_a_r_g_e_t_s': Object of class '"marrayInfo"', description of target
          samples hybridized to the arrays.

_M_e_t_h_o_d_s:

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

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

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

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

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

     _m_a_L_a_y_o_u_t 'signature(object = "marrayTwo")':  slot accessor method.

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

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

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

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

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

     _m_a_N_s_a_m_p_l_e_s 'signature(object = "marrayTwo")': slot accessor
          method.

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

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

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

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

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

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

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

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

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

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

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

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

     _m_a_S_u_b<- 'signature(object = "marrayTwo")': slot assignment method. 

     _m_a_T_a_r_g_e_t_s 'signature(object = "marrayTwo")': slot accessor method.

     _m_a_T_a_r_g_e_t_s<- 'signature(object = "marrayTwo", value =
          "marrayInfo")': slot assignment method. 

     _m_a_X 'signature(object = "marrayTwo")': slot accessor method.

     _m_a_X<- 'signature(object = "marrayTwo", value = "matrix")': slot
          assignment method. 

     _m_a_Y 'signature(object = "marrayTwo")': slot accessor method.

     _m_a_Y<- 'signature(object = "marrayTwo", value = "matrix")': slot
          assignment method. 

     _p_r_i_n_t 'signature(x = "marrayTwo")': print method for '"marrayTwo"'
          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:

     'marrayLayout', 'marrayRaw', 'marrayNorm', 'marrayInfo',
     'marraySpots', 'print-methods', '[-methods'.

_E_x_a_m_p_l_e_s:

     ## See marrayRaw

