marrayFit-class           package:stepNorm           R Documentation

_C_l_a_s_s "_m_a_r_r_a_y_F_i_t", _s_t_o_r_i_n_g _p_a_r_a_m_e_t_e_r_s _a_n_d _r_e_s_u_l_t_s _o_f
_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 _d_a_t_a

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

     A simple list-based class for the storage of parameters and
     results of normalization of cDNA microarray data.

_C_r_e_a_t_i_n_g _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('marrayFit',
     fit)' where 'fit' is a list. Objects of 'marrayFit' in the
     'StepNorm' package are typically created by functions 'fitWithin'
     and 'fit2DWithin'.

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

     This class contains no slots, but objects should contain the
     following list components:

     _v_a_r_f_u_n : A character vector of names of predictor variables.

     _x : A numeric matrix of predictor variables.

     _y : A numeric matrix of repsonses.

     _r_e_s_i_d_u_a_l_s : A numeric matrix of normalized values (typically log
          ratios (M)).

     _f_i_t_t_e_d : A numeric matrix of the fitted values.

     _e_n_p : The equivalent number of parameters; see 'loess'.

     _d_f._r_e_s_i_d_u_a_l : The residual degrees of freedom.

     _f_u_n : A character string indicating the name of the function used
          for normalization.

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

     This class inherits directly from class 'list' so any operation
     appropriate for lists will work on objects of this class.

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

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu

_S_e_e _A_l_s_o:

     'fitWithin', 'fit2DWithin'.

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

     ## load in swirl data
     data(swirl)

     ## median normalization for the first slide of the swirl data
     medWithin <- fitWithin(fun="medfit")
     ## medFit is an object of class marrayFit
     medFit <- medWithin(swirl[,1])
     ## normalized ratios is stored in:
     norm.M <- medFit$residuals

