marrayNorm-class        package:marrayClasses        R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_N_o_r_m", _c_l_a_s_s_e_s _a_n_d _m_e_t_h_o_d_s _f_o_r _p_o_s_t-_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 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 the average log-intensities A, the
     normalized log-ratios M, the location and scale normalization
     values, 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('marrayNorm','
      '    maA        = ...., # Object of class matrix'
      '    maM        = ...., # Object of class matrix'
      '    maMloc     = ...., # Object of class matrix'
      '    maMscale   = ...., # 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'
      '    maNormCall = ...., # Object of class call'
      '  )'

_S_l_o_t_s:

     '_m_a_A': Object of class '"matrix"', average log-intensities (base
          2) A, rows correspond to spotted probe sequences, columns to
          arrays in the batch.

     '_m_a_M': Object of class '"matrix"', intensity log-ratios (base 2)
          M, rows correspond to spotted probe sequences, columns to
          arrays in the batch.

     '_m_a_M_l_o_c': Object of class '"matrix"', location normalization
          values, rows correspond to spotted probe sequences, columns
          to arrays in the batch.

     '_m_a_M_s_c_a_l_e': Object of class '"matrix"',  scale normalization
          values, 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 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_a_N_o_r_m_C_a_l_l': Object of class '"call"', function call for
          normalizing the batch of arrays.

_M_e_t_h_o_d_s:

     [ 'signature(x = "marrayNorm")':  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'. 

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

     _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_A 'signature(object = "marrayNorm")': slot accessor method.

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

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

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

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

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

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

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

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

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

     _m_a_M 'signature(object = "marrayNorm")': slot accessor method.

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

     _m_a_M_l_o_c 'signature(object = "marrayNorm")': slot accessor method.

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

     _m_a_M_s_c_a_l_e 'signature(object = "marrayNorm")': slot accessor method.

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

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

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

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

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

     _m_a_N_o_r_m_C_a_l_l 'signature(object = "marrayNorm")': slot accessor
          method.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

     _p_r_i_n_t 'signature(x = "marrayNorm")': print method for
          '"marrayNorm"' 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', 'marrayInfo', 'marraySpots',
     'marrayTwo', 'exprSet-class', 'print-methods', '[-methods',
     'coerce-methods'.

_E_x_a_m_p_l_e_s:

     # Examples use swirl dataset, for description type ? swirl

     # data(swirl)

     # Normalization is done using functions from the marrayNorm package
     # library(marrayNorm)

     # Within-print-tip-group loess location normalization
     # mnorm<-maNorm(swirl[,2:3],norm="p")

     # Object of class marrayNorm for the second and third swirl arrays
     # mnorm

     # Function call
     # maNormCall(mnorm)

     #  Object of class marrayInfo -- Probe sequences
     # maGnames(mnorm)

     #  Object of class marrayInfo -- Target samples
     # maTargets(mnorm)

     # Density plot of log-ratios M for third array
     # plot(density(maM(mnorm[,2])), lwd=2, col=2, main="Density plots of log-ratios M")
     # lines(density(maM(swirl[,3])), lwd=2)
     # abline(v=0)
     # legend(2,1,c("Pre-normalization","Post-normalization"))

