find.params.pdnn          package:affypdnn          R Documentation

_A _f_u_n_c_t_i_o_n _t_o _f_i_n_d _t_h_e _e_x_p_e_r_i_m_e_n_t _s_p_e_c_i_f_i_c _P_D_N_N _p_a_r_a_m_e_t_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     A function to find the paramaters specific to the chips in an
     AffyBatch object.

_U_s_a_g_e:

     find.params.pdnn(abatch, params.chiptype, optim.method = "BFGS", verbose = TRUE, give.warnings=TRUE)

_A_r_g_u_m_e_n_t_s:

  abatch: an instance of 'Affybatch-class'. 

params.chiptype: chip-type specific parameters (see details)

optim.method: method for the optimization function 'optim'. When
          'FALSE', a steepest-descent method of our own is used.

 verbose: verbosity ('TRUE' or 'FALSE') 

give.warnings: report probeset IDs in the 'abatch' that could not be
          found in the 'params.chiptype'

_D_e_t_a_i_l_s:

     This function fits PDNN parameters that are specific to
     experimental values. The parameters common to all the chips of a
     certain type are returned by the function 'pdnn.params.chiptype'.
     If 'NULL', the parameter files included in the package will be
     used whenever possible...

_V_a_l_u_e:

     A list of 

  lambda: The lambda's

      Bs: The B's

      Ns: The N's

      Fs: The F's

_R_e_f_e_r_e_n_c_e_s:

     Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of
     molecular interactions on short oligonucleotide arrays, 2003,
     Nature Biotech., vol. 21, n.7

_S_e_e _A_l_s_o:

     'pdnn.params.chiptype', 'generateExprVal.method.pdnn'

_E_x_a_m_p_l_e_s:

     ## load a chip-specific parameter file
     ## (as returned by the function pdnn.params.chiptype)
     data(hgu95av2.pdnn.params)

     ## load experimental data
     library(affydata)
     data(Dilution)

     ## one CEL to go faster
     afbatch <- Dilution[, 1]
     params <- find.params.pdnn(afbatch, hgu95av2.pdnn.params, optim.method =
     FALSE, give.warnings=FALSE)

