fast.bkg                package:gcrma                R Documentation

_I_n_t_e_r_n_a_l _f_u_n_c_t_i_o_n_s _f_o_r _j_u_s_t_G_C_R_M_A

_D_e_s_c_r_i_p_t_i_o_n:

     These are internal functions for justGCRMA that are called based
     on memory or speed constraints.

_U_s_a_g_e:

     fast.bkg(filenames, pm.affinities, mm.affinities, index.affinities,
     type, minimum, optical.correct, verbose, k, rho, correction, stretch,
     fast, cdfname, read.verbose)
     mem.bkg(filenames, pm.affinities, mm.affinities, index.affinities, type,
     minimum, optical.correct, verbose, k, rho, correction, stretch, fast,
     cdfname, read.verbose)

_A_r_g_u_m_e_n_t_s:

filenames: A list of cel files.

pm.affinities: Values passed from 'compute.affinities'.

mm.affinities: Values passed from 'compute.affinities'.

index.affinities: Values passed from 'compute.affinities'.

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

 minimum: A minimum value to be used for 'optical.correct'.

optical.correct: Logical value. If 'TRUE', optical background
          correction is performed.

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

       k: A tuning factor.

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

correction: 

 stretch: 

    fast: Logical value. If 'TRUE', then a faster ad hoc algorithm is
          used.

 cdfname: Used to specify the name of an alternative cdf package. If
          set to 'NULL', the usual cdf package based on Affymetrix'
          mappings will be used. Note that the name should not include
          the 'cdf' on the end, and that the corresponding probe
          package is also required to be installed. If either package
          is missing an error will result.

read.verbose: Logical value. If 'TRUE', a message is returned as each
          celfile is read in.

_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 tuning factor 'k' will have different meanings if one uses the
     fast (add-hoc) algorithm or the empirical Bayes approach. See Wu
     et al. (2003)

_V_a_l_u_e:

     An 'ExpressionSet'.

_A_u_t_h_o_r(_s):

     James W. MacDonald <jmacdon@med.umich.edu>

_S_e_e _A_l_s_o:

     'gcrma'