marrayInfo-class           package:marray           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.

     _p_r_i_n_t 'signature(x = "marrayInfo")': print method for
          '"marrayInfo"' class.

_A_u_t_h_o_r(_s):

     Jean Yang and Sandrine Dudoit

_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'.

_E_x_a_m_p_l_e_s:

     ## See marrayRaw