threshold              package:MixThres              R Documentation

_T_h_r_e_s_h_o_l_d _H_y_b_r_i_d_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Define a threshold hybridization in DNA microarray experiments.

_U_s_a_g_e:

     threshold(MixThres, crit = 1e-04, fileGRAPH = NULL, fileOUT = NULL, sep = "\t", ...)

_A_r_g_u_m_e_n_t_s:

MixThres    : an object of class MixThres. 

crit        : precision used to define the hybridization threshold 

fileGRAPH   : the name of the file where graphic is created. If
          fileGRAPH=NULL no graphic is made. 

fileOUT     : the name of the file where output are created. If
          fileOUT=NULL no output file is created. 

sep         : the field separator string used for writing the output
          file. Values within each row of x are separated by this
          string. 

...       : others arguments to write.table 

_D_e_t_a_i_l_s:

     The threshold above which a probe is declared as being hybridized
     is defined as following : 

     T(crit) = max(y_g |{k^*_g}<widehat{K} exists s epsilon
     (1,...,k^*_{g-1}), widehat{tau}_{sg} >=q crit) 
      In other words, intensity values are ranked by descending order,
     for each probe _g_ $k^*_g$ is determined using the Maximum A
     Posteriori rule. Then if $k^*_g$ differs from the component with
     the highest mean $\widehat{K}$, the posterior probability of
     belonging to each component with lower mean than $mu_{k^*_g}$ is
     calculated. The threshold is then defined as the first intensity
     value such that one of the calculated posterior probabilities is
     greater than _crit_.

_V_a_l_u_e:

     an object of class MixThres. Three components are added : 

threshold   : the hybridization threshold.

crit        : the precision value associated to the hybridization
          threshold.

Hybrid      : the hybridization index precising wether the spot is
          hybridized (1) or not (0).

_A_u_t_h_o_r(_s):

     J. Aubert

_R_e_f_e_r_e_n_c_e_s:

     Picard et al., Using mixture models to define a hybridization
     threshold in DNA microarray experiments.

_S_e_e _A_l_s_o:

     'hybridization'

