ParameterList-class          package:CALIB          R Documentation

_C_l_a_s_s "_P_a_r_a_m_e_t_e_r_L_i_s_t" - _L_i_s_t _t_o _s_t_o_r_e _a_l_l _t_h_e _p_a_r_a_m_e_t_e_r_s

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

     A simple list-based class for storing all the model parameters of
     a  batch of microarray.

_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("ParameterList",
     parameter)'  where parameter is a list. In the CALIB package,
     ParameterList objects are  normally generated by function
     'estimateParameter'.

_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects should contain the following list components:

     '_M_u_S': Spot parameter. Mean of spot capacity.

     '_K_a': Hybridization constant.

     '_P_1': Respective slope of the linear dye saturation function. It
          is different for different dyes.

     '_P_2': Respective intercept of the linear dye saturation function.
          It is different for different dyes

     '_S_i_g_m_a_A': Standard deviation of additive error. It is different
          for different dyes.

     '_S_i_g_m_a_M': Standard deviation of multiplicative error.

     '_S_i_g_m_a_S': Spot parameter. Standard deviation of spot capacity.

     '_S_p_o_t_E_r_r_o_r': numeric matrix containing spot error of all external
          control spikes on arrays

     '_M_e_t_h_o_d': boolean values indicating the way to calculate the
          measured  intensities. It contains two subfields which are
          both logical value: BC and  Area. BC indicates whether
          background corrected measured intensities are used. Area
          indicates whether spot area is used to calculate measured
          intensities. 

     '_E_r_r_o_r_M_o_d_e_l': a character to represent the distribution of spot
          capacity. "L" means spot capacity follows 'log normal'
          distribution. "N" means spot  capacity follows 'normal'
          distribution.

     '_g_e_n_e_s': data.frame containing information on spikes spotted on
          the arrays. Should include a character column Name containing
          names for all the spikes.

     See reference for more detailed explaination for these list
     components.

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class
     '"list"'.

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

     This class inherits directly from class List. However since it
     represents the parameters  of the calibration model for arrays, it
     makes on sense to run functions like 'dim',  'dimnames',or 'merge'
     on this class.  Therefore, only some operations appropriate for
     list will work on objects of this class.  ParameterList objects
     can be 'cbind' and 'show' in a compact way.

     ParameterList objects are used on functions such as
     'normalizeData' or on some other data visualization functions like
     'plotSpikeHI' in the CALIB package.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006)  A
     calibration method for estimating absolute expression levels from 
     microarray data. Bioinformatics  22: 1251-1258.

