vsn                   package:vsn                   R Documentation

_C_l_a_s_s _t_o _c_o_n_t_a_i_n _r_e_s_u_l_t _o_f _a _v_s_n _f_i_t

_D_e_s_c_r_i_p_t_i_o_n:

     Class to contain result of a vsn fit

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new("vsn")' 'vsn2(x)' with 'x' being an 'ExpressionSet'.

_S_l_o_t_s:

     '_c_o_e_f_f_i_c_i_e_n_t_s': A 3D array of size (number of strata) x (number of
          columns of the data matrix) x 2 containing fitted
          normalization parameters (see vignette).

     '_s_t_r_a_t_a': A factor of length 0 or n. If its length is n, then its
          levels correspond to different normalization strata (see
          vignette).

     '_m_u': A numeric vector of length n with the fitted parameters
          $\hat{mu}_k$, $k=1,...,n$.

     '_s_i_g_s_q': A numeric scalar, $\hat{sigma}$.

     '_h_x': A numeric matrix with 0 or n rows. If the number of rows is
          n, then 'hx' contains the transformed data matrix.

     '_l_b_f_g_s_b': An integer scalar containing the return code from the
          L-BFGS-B optimizer.

_M_e_t_h_o_d_s:

     '[' Subset

     '_d_i_m' Get dimensions of data matrix.

     '_n_r_o_w' Get number of rows of data matrix.

     '_n_c_o_l' Get number of columns of data matrix.

     '_s_h_o_w' Print a summary of the object

     '_e_x_p_r_s' Accessor to slot 'hx'.

     '_c_o_e_f', '_c_o_e_f_f_i_c_i_e_n_t_s' Accessors to slot 'coefficients'.

_A_u_t_h_o_r(_s):

     Wolfgang Huber <URL: http://www.ebi.ac.uk/huber>

_S_e_e _A_l_s_o:

     'vsn2'

_E_x_a_m_p_l_e_s:

       data("kidney")
       v = vsn2(kidney)
       show(v)
       dim(v)
       v[1:10, ]

