Xprep                  package:SAGx                  R Documentation

_C_a_l_c_u_l_a_t_i_o_n _o_f _i_n_p_u_t _t_o _s_t_a_t._b_a_y_e_s_i_a_n _s_t_a_r_t_i_n_g _f_r_o_m _l_i_n_e_a_r _m_o_d_e_l

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

     The function fits a linear model to a microarray data matrix.

_U_s_a_g_e:

     Xprep(indata=M, formula=~as.factor(g), contrast=c(0,1), design=NULL,Vars=NULL)

_A_r_g_u_m_e_n_t_s:

  indata: The data matrix

 formula: a linear model formula in the lm format

contrast: a vector defining the contrast of interest

  design: the design matrix

    Vars: if not null the variance of the se is estimated through
          jacknife.

_D_e_t_a_i_l_s:

     As of v1.5 the code has been improved in terms of speed and takes
     advantage of built-in R functions. This incereases the efficiency
     of e.g. samroc.

_V_a_l_u_e:

     a list with the entries  

    Mbar: estimate of the contrast

    Vest: the error variance

       k: inverse of the scale factor turning Vest into a standard
          error

       f: the degrees of freedom of Vest

  design: the design matrix

   Varse: The variance of the standard error

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

     Per Broberg

