MIAME                package:Biobase                R Documentation

_C_l_a_s_s _f_o_r _S_t_o_r_i_n_g _M_i_c_r_o_a_r_r_a_y _E_x_p_e_r_i_m_e_n_t _I_n_f_o_r_m_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Class 'MIAME' covers MIAME entries that are not covered by other
     classes in Bioconductor. Namely, experimental design, samples,
     hybridizations, normalization controls, and pre-processing
     information.

_S_l_o_t_s:


     '_n_a_m_e': Object of class 'character' containing the experimenter
          name

     '_l_a_b': Object of class 'character' containing the laboratory where
          the experiment was conducted

     '_c_o_n_t_a_c_t': Object of class 'character' containing contact
          information for lab and/or experimenter

     '_t_i_t_l_e': Object of class 'character' containing a single-sentence
          experiment title 

     '_a_b_s_t_r_a_c_t': Object of class 'character' containing an abstract
          describing the experiment

     '_u_r_l': Object of class 'character' containing a URL for the
          experiment

     '_s_a_m_p_l_e_s': Object of class 'list' containg information about the
          samples

     '_h_y_b_r_i_d_i_z_a_t_i_o_n_s': Object of class 'list' containing information
          about the hybridizations

     '_n_o_r_m_C_o_n_t_r_o_l_s': Object of class 'list' containing information
          about the controls such as house keeping genes

     '_p_r_e_p_r_o_c_e_s_s_i_n_g': Object of class 'list' containing information
          about the pre-processing steps used on the raw data from this
          experiment

     '_p_u_b_M_e_d_I_d_s': Object of class 'character' listing strings of PubMed
          identifiers of papers relevant to the dataset

     '_o_t_h_e_r': Object of class 'list' containing other information for
          which none of the above slots does not applies

_M_e_t_h_o_d_s:

     Class-specific methods:

     '_a_b_s_t_r_a_c_t(_M_I_A_M_E)': An accessor function for 'abstract'.

     '_c_o_m_b_i_n_e(_M_I_A_M_E,_M_I_A_M_E)': Combine two objects of 'MIAME-class',
          issuing warnings when ambiguities encountered.

     '_e_x_p_i_n_f_o(_M_I_A_M_E)': An accessor function for 'name', 'lab',
          'contact', 'title', and 'url'.

     '_h_y_b_r_i_d_i_z_a_t_i_o_n_s(_M_I_A_M_E)': An accessor function for
          'hybridizations'.

     '_n_o_r_m_C_o_n_t_r_o_l_s(_M_I_A_M_E)': An accessor function for 'normControls'.

     '_n_o_t_e_s(_M_I_A_M_E), _n_o_t_e_s(_M_I_A_M_E) <- _v_a_l_u_e': Accessor functions for
          'other'. 'notes(MIAME) <- character' _appends_ character to
          notes; use 'notes(MIAME) <- list' to replace the notes
          entirely.

     '_o_t_h_e_r_I_n_f_o(_M_I_A_M_E)': An accessor function for 'other'.

     '_p_r_e_p_r_o_c(_M_I_A_M_E)': An accessor function for 'preprocessing'.

     '_p_u_b_M_e_d_I_d_s(_M_I_A_M_E), _p_u_b_M_e_d_I_d_s(_M_I_A_M_E) <- _v_a_l_u_e': Accessor function
          for 'pubMedIds'.

     '_s_a_m_p_l_e_s(_M_I_A_M_E)': An accessor function for 'samples'.

     Standard generic methods:

     '_u_p_d_a_t_e_O_b_j_e_c_t(_o_b_j_e_c_t, ..., _v_e_r_b_o_s_e=_F_A_L_S_E)' Update instance to
          current version, if necessary. See 'updateObject'

     '_i_s_C_u_r_r_e_n_t(_o_b_j_e_c_t)' Determine whether version of object is
          current. See 'isCurrent'

     '_i_s_V_e_r_s_i_o_n_e_d(_o_b_j_e_c_t)' Determine whether object contains a
          'version' string describing its structure . See 'isVersioned'

     '_s_h_o_w(_M_I_A_M_E)': Renders information about the MIAME information 

_A_u_t_h_o_r(_s):

     Rafael A. Irizarry

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.mged.org/Workgroups/MIAME/miame_1.1.html>

_S_e_e _A_l_s_o:

     'class:characterORMIAME', 'read.MIAME'

