marrayRaw-class            package:marray            R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_R_a_w", _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _p_r_e-_n_o_r_m_a_l_i_z_a_t_i_o_n _c_D_N_A _m_i_c_r_o_a_r_r_a_y _i_n_t_e_n_s_i_t_y _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This class represents pre-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 the green (Cy3) and red (Cy5) foreground and
     background intensities, the layout of the arrays, and descriptions
     of the target samples hybridized to the arrays and 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('marrayRaw','
      '    maRf      = ...., # Object of class matrix'
      '    maGf      = ...., # Object of class matrix'
      '    maRb      = ...., # Object of class matrix'
      '    maGb      = ...., # Object of class matrix'
      '    maW       = ...., # Object of class matrix'
      '    maLayout  = ...., # Object of class marrayLayout'
      '    maGnames  = ...., # Object of class marrayInfo'
      '    maTargets = ...., # Object of class marrayInfo'
      '    maNotes   = ...., # Object of class character'
      '  )'

_S_l_o_t_s:

     '_m_a_R_f': Object of class '"matrix"', red foreground intensities,
          rows correspond to spotted probe sequences, columns to arrays
          in the batch.

     '_m_a_G_f': Object of class '"matrix"', green foreground intensities,
          rows correspond to spotted probe sequences, columns to arrays
          in the batch. 

     '_m_a_R_b': Object of class '"matrix"', red background intensities,
          rows correspond to spotted probe sequences, columns to arrays
          in the batch. 

     '_m_a_G_b': Object of class '"matrix"', green background intensities,
          rows correspond to spotted probe sequences, columns to arrays
          in the batch. 

     '_m_a_W': Object of class '"matrix"', spot quality weights, 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_G_n_a_m_e_s': Object of class '"marrayInfo"', description of spotted
          probe sequences.

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

     '_m_a_N_o_t_e_s': Object of class '"character"',  any notes concerning
          the microarray experiments, e.g. hybridization or scanning
          conditions.

_M_e_t_h_o_d_s:

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

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

     _m_a_A 'signature(object = "marrayRaw")': function which computes
          average log-intensities (base 2) A for an object of class
          '"marrayRaw"'.

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

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

     _m_a_G_b 'signature(object = "marrayRaw")': slot accessor method.

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

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

     _m_a_G_f 'signature(object = "marrayRaw")': slot accessor method.

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

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

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

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

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

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

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

     _m_a_L_G 'signature(object = "marrayRaw")': method which computes
          green log-intensities (base 2) for an object of class
          '"marrayRaw"'.

     _m_a_L_R 'signature(object = "marrayRaw")': method  which computes red
          log-intensities (base 2) for an object of class
          '"marrayRaw"'.

     _m_a_M 'signature(object = "marrayRaw")': method which computes
          intensity log-ratios (base 2) M for an object of class
          '"marrayRaw"'.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

     _m_a_R_b 'signature(object = "marrayRaw")': slot accessor method.

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

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

     _m_a_R_f 'signature(object = "marrayRaw")': slot accessor method. 

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

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

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

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

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

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

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

     _m_a_W 'signature(object = "marrayRaw")': slot accessor method.

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

     _p_r_i_n_t 'signature(x = "marrayRaw")':  print method for
          '"marrayRaw"' 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', 'marrayNorm', 'marrayInfo'.

_E_x_a_m_p_l_e_s:

     # Examples use swirl dataset, for description type ? swirl
     require(limma)
     data(swirl)

     # Object of class marrayRaw for the 4 swirl arrays
     swirl

     # Object of class marrayLayout
     maLayout(swirl)

     # Access only the first 100 spots of the third array
     swirl[1:100,3]

     # Accessor methods -- How many spots on the array
     maNspots(swirl)

     # Density plot of log-ratios M for third array
     plot(density(maM(swirl[,3])))

     # Assignment methods -- Replace maNotes slot
     maNotes(swirl)
     maNotes(swirl)<-"This is a zebrafish microarray"
     maNotes(swirl)

     # Coerce methods -- Convert marrayRaw object into exprSet
     ## Load package convert
     ## library(convert)
     ## e<-as(swirl, "exprSet")
     ## e