compute.affinities           package:gcrma           R Documentation

_P_r_o_b_e _A_f_f_i_n_i_t_y _c_o_m_p_u_t_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     An internal function to calculate probe affinities from their
     sequences.

_U_s_a_g_e:

     compute.affinities(cdfname,verbose=TRUE)

     check.probes(probepackage,cdfname)

_A_r_g_u_m_e_n_t_s:

 cdfname: Object of class 'character' representing the name of 'CDF'
          file associated with the arrays in the 'AffyBatch'.

probepackage: 'character' representing the name of the package with the
          probe sequence information.

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

_D_e_t_a_i_l_s:

     The affinity of a probe is described as the sum of
     position-dependent base affinities. Each base at each position
     contributes to the total affinity of a probe in an additive
     fashion. For a given type of base, the positional effect is
     modeled as a spline function with 5 degrees of freedom.

     'check.probes' makes sure things are matching as they should.

_V_a_l_u_e:

     'compute.affinities' returns an 'AffyBatch' with the affinities
     for PM probes in the pm locations and the affinities for MM probes
     in the mm locations. NA  will be added for probes with no sequence
     information.

_A_u_t_h_o_r(_s):

     Rafeal Irizarry

_R_e_f_e_r_e_n_c_e_s:

     Hekstra, D., Taussig, A. R., Magnasco, M., and Naef, F. (2003)
     Absolute mRNA concentrations from sequence-specific calibration of
     oligonucleotide array. Nucleic Acids Research, 31. 1962-1968.

_S_e_e _A_l_s_o:

     'gcrma,affinity.spline.coefs'