gcrma.engine              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 all arrays in
     the dataset share the same probe affinity information. It takes
     matrices of PM probe intensities, MM probe intensities, other
     negative control probe intensities(optional) and the associated
     probe affinities, and return one matrix of non-specific binding
     corrected PM probe intensities.

_U_s_a_g_e:

     gcrma.engine(pms,mms,ncs=NULL,
                              pm.affinities=NULL,mm.affinities=NULL,anc=NULL,
                              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=FALSE)

_A_r_g_u_m_e_n_t_s:

     pms: The matrix of PM intensities

     mms: The matrix of MM intensities

     ncs: The matrix of negative control probe intensities. When left
          as'NULL', the MMs are considered the negative control probes.

pm.affinities: The vector of PM probe affinities. Note: This can be
          shorter than the number of rows in 'pms' when some probes do
          not have sequence information provided.

mm.affinities: The vector of MM probe affinities.

     anc: The vector of Negative Control probe affinities. This is
          ignored if MMs are used as negative controls ('ncs=NULL')

    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.engine2