gcrma.engine2             package:gcrma             R Documentation

_G_C_R_M_A _b_a_c_k_g_r_o_u_n_d _a_d_j_u_s_t _e_n_g_i_n_e(_i_n_t_e_r_n_a_l _f_u_n_c_t_i_o_n)

_D_e_s_c_r_i_p_t_i_o_n:

     This function adjust for non-specific binding when each array has
     its own probe affinity information. It takes an AffyBatch object
     of probe intensities and an AffyBatch of probe  affinity, returns
     one matrix of non-specific binding corrected PM probe intensities.

_U_s_a_g_e:

     gcrma.engine2(object,pmIndex=NULL,mmIndex=NULL,
                   NCprobe=NULL,affinity.info,
                   type=c("fullmodel","affinities","mm","constant"),
                   k=6*fast+0.5*(1-fast),
                   stretch=1.15*fast+1*(1-fast),correction=1,GSB.adjust=TRUE,rho=0.7,
                   verbose=TRUE,fast=TRUE)

_A_r_g_u_m_e_n_t_s:

  object: an 'AffyBatch'. Note: this is an internal function. Optical
          noise should have been corrected for. 

 pmIndex: Index of PM probes.This will be computed within the function
          if left 'NULL'

 mmIndex: Index of MM probes.This will be computed within the function
          if left 'NULL'

 NCprobe: 

affinity.info: 'NULL' or an 'AffyBatch' containing the affinities in
          the 'exprs' slot. This object can be created using the
          function 'compute.affinities'.

    type: "fullmodel" for sequence and MM model. "affinities" for
          sequence information only. "mm" for using MM without sequence
          information.

       k: A tuning factor.

 stretch: 

correction: .

GSB.adjust: Logical value. If 'TRUE', probe effects in specific binding
          will be adjusted.

     rho: correlation coefficient of log background intensity in a pair
          of pm/mm probes. Default=.7

 verbose: Logical value. If 'TRUE' messages about the progress of the
          function is printed.

    fast: Logicalvalue. If 'TRUE' a faster add-hoc algorithm is used.

_D_e_t_a_i_l_s:

     Note that this expression measure is given to you in log base 2
     scale. This differs from most of the other expression measure
     methods.

     The tunning factor 'k' will have different meainngs if one uses
     the fast (add-hoc) algorithm or the empirical bayes approach. See
     Wu et al. (2003)

_V_a_l_u_e:

     A matrix of PM intensties.

_A_u_t_h_o_r(_s):

     Rafeal Irizarry & Zhijin Wu

_S_e_e _A_l_s_o:

     gcrma.engine