affyVstRma               package:lumi               R Documentation

_P_r_e_p_r_o_c_e_s_s _A_f_f_y_m_e_t_r_i_x _d_a_t_a _b_y _i_n_t_e_g_r_a_t_i_n_g _V_S_T _w_i_t_h _R_M_A _m_e_t_h_o_d

_D_e_s_c_r_i_p_t_i_o_n:

     Preprocess Affymetrix data by integrating VST with RMA method

_U_s_a_g_e:

     affyVstRma(afbatch, bgcorrect.method = "none", bgcorrect.param = list(), VST.param = list(), verbose = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

 afbatch: a vector of CEL file names or an AffyBatch object, see
          'AffyBatch-class' 

bgcorrect.method: the name of the background adjustment method 

bgcorrect.param: a list of parameters for bgcorrect.method (if
          needed/wanted) 

VST.param: a list of parameters for 'vst' method 

 verbose: logical value. If TRUE it writes out some messages. 

     ...: other parameters used by 'rma' function 

_D_e_t_a_i_l_s:

     This function basically integrates the VST (variance stabilizing
     transformation) transformation into the rma function in the affy
     package. The variance stabilization is based on the mean and
     variance relations of pixel intensities of each probe.

_V_a_l_u_e:

     Return an object of class ExpressionSet.

_N_o_t_e:

     The performance of this function is still under evaluation.

_A_u_t_h_o_r(_s):

     Pan Du

_S_e_e _A_l_s_o:

     'expresso' and 'vst'

