preprocess              package:affyPLM              R Documentation

_B_a_c_k_g_r_o_u_n_d _c_o_r_r_e_c_t _a_n_d _N_o_r_m_a_l_i_z_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function pre-processes an 'AffyBatch'.

_U_s_a_g_e:

     preprocess(object,subset=NULL, normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",background.param = list(),normalize.param=list(),verbosity.level=0)

_A_r_g_u_m_e_n_t_s:

  object: an 'AffyBatch'

  subset: a vector with the names of probesets to be used. If NULL then
          all probesets are used.

normalize: logical value. If 'TRUE' normalize data using quantile
          normalization

background: logical value. If 'TRUE' background correct using RMA
          background correction

background.method: name of background method to use.

normalize.method: name of normalization method to use.

background.param: list of parameters for background correction methods

normalize.param: list of parameters for normalization methods

verbosity.level: An integer specifying how much to print out. Higher
          values indicate more verbose. A value of 0 will print nothing

_D_e_t_a_i_l_s:

     This function carries out background correction and normalization
     pre-processing steps. It does not summarize to produce gene
     expression measures. All the same pre-processing methods supplied
     by 'threestep' are supported by this function.

_V_a_l_u_e:

     An 'AffyBatch'

_A_u_t_h_o_r(_s):

     Ben Bolstad bmb@bmbolstad.com

_R_e_f_e_r_e_n_c_e_s:

     Bolstad, BM (2004) _Low Level Analysis of High-density
     Oligonucleotide Array Data: Background, Normalization and
     Summarization_. PhD Dissertation. University of California,
     Berkeley.

_S_e_e _A_l_s_o:

     'expresso', 'rma'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)

       # should be equivalent to the bg and norm of rma()
       abatch.preprocessed <- preprocess(Dilution)
     }

