marrayInfo-class        package:marrayClasses        R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_I_n_f_o", _d_e_s_c_r_i_p_t_i_o_n _o_f _t_a_r_g_e_t _s_a_m_p_l_e_s _o_r _s_p_o_t_t_e_d _p_r_o_b_e _s_e_q_u_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class is used to store information on target samples
     hybridized to a batch of arrays or probe sequences spotted onto
     these arrays. It is not specific to the microarray context.

_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('marrayInfo','
      '    maLabels = ...., # Object of class character'
      '    maInfo   = ...., # Object of class data.frame'
      '    maNotes  = ...., # Object of class character'
      '  )'

_S_l_o_t_s:

     '_m_a_L_a_b_e_l_s': Object of class '"character"', vector of spot or array
          labels.

     '_m_a_I_n_f_o': Object of class '"data.frame"'. If the object of class
          '"marrayInfo"' is used to describe probe sequences, rows of
          'maInfo' correspond to spots and columns to various gene
          identifiers and annotations.  If the object of class
          '"marrayInfo"' is used to describe target samples hybridized
          to the arrays, rows of 'maInfo' correspond to arrays and
          columns to various descriptions of the hybridizations, e.g.,
          names of Cy3 and Cy5 samples, labels for the arrays etc.

     '_m_a_N_o_t_e_s': Object of class '"character"', any notes on the target
          samples or spotted probe sequences.

_M_e_t_h_o_d_s:

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

     _m_a_G_n_a_m_e_s<- 'signature(object = "marrayRaw", value =
          "marrayInfo")': slot assignment method.

     _m_a_G_n_a_m_e_s<- 'signature(object = "marrayNorm", value =
          "marrayInfo")': slot assignment method.

     _m_a_G_n_a_m_e_s<- 'signature(object = "marraySpots", value =
          "marrayInfo")': slot assignment method.

     _m_a_I_n_f_o 'signature(object = "marrayInfo")': slot accessor method.

     _m_a_I_n_f_o<- 'signature(object = "marrayInfo", value = "data.frame")':
          slot assignment method.

     _m_a_L_a_b_e_l_s 'signature(object = "marrayInfo")': slot accessor method.

     _m_a_L_a_b_e_l_s<- 'signature(object = "marrayInfo", value =
          "character")': slot assignment method.

     _m_a_L_a_b_e_l_s<- 'signature(object = "marrayInfo", value = "numeric")':
          slot assignment method.

     _m_a_N_o_t_e_s 'signature(object = "marrayInfo")': slot accessor method.

     _m_a_N_o_t_e_s<- 'signature(object = "marrayInfo", value = "character")':
          slot assignment method.

     _m_a_T_a_r_g_e_t_s<- 'signature(object = "marrayRaw", value =
          "marrayInfo")': slot assignment method.

     _m_a_T_a_r_g_e_t_s<- 'signature(object = "marrayNorm", value =
          "marrayInfo")': slot assignment method.

     _m_a_T_a_r_g_e_t_s<- 'signature(object = "marrayTwo", value =
          "marrayInfo")': slot assignment method.

     _p_r_i_n_t 'signature(x = "marrayInfo")': print method for
          '"marrayInfo"' 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', 'marraySpots',
     'marrayTwo', 'exprSet-class', 'print-methods', '[-methods'.

_E_x_a_m_p_l_e_s:

     ## See marrayRaw

