affyExpresso              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 _e_x_p_r_e_s_s_o _m_e_t_h_o_d

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

     Preprocess Affymetrix data by integrating VST with expresso method

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

     affyExpresso(afbatch, bg.correct = TRUE, bgcorrect.method = NULL, bgcorrect.param = list(), variance.stabilize = TRUE, varianceStabilize.method = c("vst", "log2", "cubicRoot"), varianceStabilize.param = list(), normalize = TRUE, normalize.method = NULL, normalize.param = list(), pmcorrect.method = NULL, pmcorrect.param = list(), summary.method = NULL, summary.param = list(), summary.subset = NULL, 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'  

bg.correct: a boolean to express whether background correction is
          wanted or not 

bgcorrect.method: the name of the background adjustment method 

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

variance.stabilize: a boolean to express whether variance stabilization
          is wanted or not 

varianceStabilize.method: the name of the variance stabilizing
          transform, same as 'lumiT' function 

varianceStabilize.param: a list of parameters for transformation method            

normalize: normalization step wished or not 

normalize.method: the normalization method to use 

normalize.param: a list of parameters to be passed to the normalization
          method (if wanted) 

pmcorrect.method: the name of the PM adjustement method 

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

summary.method: the method used for the computation of expression
          values 

summary.param: a list of parameters to be passed to the summary.method
          (if wanted) 

summary.subset: a list of 'affyids'. If NULL, a expression summary
          value is computed for everything on the chip 

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

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

     This function basically integrates the VST (variance stabilizing
     transformation) transformation into the expresso 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:

     'rma' and 'vst'

