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'

