marraySpots-class       package:marrayClasses       R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_S_p_o_t_s", _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _p_r_o_b_e _s_e_q_u_e_n_c_e_s _s_p_o_t_t_e_d _o_n _m_i_c_r_o_a_r_r_a_y_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class stores information on the spotted probe sequences for a
     batch of arrays. A _batch of arrays_ consists of a collection of
     arrays with the same layout  ('"marrayLayout"'). The class
     contains slots for the layout of the arrays, and a description of
     the probe sequences spotted onto 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('marraySpots','
      '    maGnames = ...., # Object of class marrayInfo'
      '    maLayout  = ...., # Object of class marrayLayout'

_S_l_o_t_s:

     '_m_a_G_n_a_m_e_s': Object of class '"marrayInfo"',  description of
          spotted probe sequences.

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

_M_e_t_h_o_d_s:

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

     _c_o_e_r_c_e 'signature(from = "marrayRaw", to = "marraySpots")': coerce
          an object of class '"marrayRaw"' into an object of class
          '"marraySpots"'. 

     _c_o_e_r_c_e 'signature(from = "marrayNorm", to = "marraySpots")':
          coerce an object of class '"marrayNorm"' into an object of
          class '"marraySpots"'.  

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

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

     _m_a_G_n_a_m_e_s 'signature(object = "marraySpots")': slot accessor
          method.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

     _p_r_i_n_t 'signature(x = "marraySpots")': print method for
          '"marraySpots"' 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',
     'marrayTwo', 'print-methods', '[-methods'.

_E_x_a_m_p_l_e_s:

     ## See marrayRaw

