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'

