threestepPLM             package:affyPLM             R Documentation

_T_h_r_e_e _S_t_e_p _e_x_p_r_e_s_s_i_o_n _m_e_a_s_u_r_e_s _r_e_t_u_r_n_e_d _a_s _a _P_L_M_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function converts an 'AffyBatch' into an 'PLMset' using a
     three step expression measure.

_U_s_a_g_e:

     threestepPLM(object,subset=NULL, normalize=TRUE,background=TRUE,background.method="RMA.2",normalize.method="quantile",summary.method="median.polish",background.param = list(),normalize.param=list(),output.param=list(), model.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.

summary.method: name of summary method to use.

background.param: list of parameters for background correction methods

normalize.param: list of parameters for normalization methods

output.param: list of parameters for output methods

model.param: list of parameters for model 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 computes the expression measure using threestep
     methods. It returns a 'PLMset'. The most important difference is
     that the PLMset allows you to access the residuals which the
     'threestep' function does not do.

_V_a_l_u_e:

     An 'PLMset'

_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', 'threestep', 'rmaPLM', 'fitPLM'

_E_x_a_m_p_l_e_s:

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

       # should be equivalent to rma()
       ## Not run: eset <- threestepPLM(Dilution)
     }

