deds.genExtra              package:DEDS              R Documentation

_G_e_n_e_r_a_t_i_n_g _E_x_t_r_a _P_a_r_a_m_e_t_e_r_s _f_o_r _T_e_s_t _S_t_a_t_i_s_t_i_c_s _F_u_n_c_t_i_o_n_s _f_o_r
_D_i_f_f_e_r_e_n_t_i_a_l _E_x_p_r_e_s_s_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     'deds.genExtra' is used to pass in extra arguments for 'comp.stat'
     and 'deds.stat.linkC', which computes various test statistics for
     differential expression in microarray data.

_U_s_a_g_e:

     deds.genExtra(classlabel, tests)

_A_r_g_u_m_e_n_t_s:

classlabel: A vector of integers corresponding to observation (column)
          class labels. For k classes, the labels must be integers
          between 0 and k-1.

   tests: A vector of character string specifying the statistics to be
          used to test differential expression. The character string
          could be any of the followings: 

            'test="t"':     one- or two-sample t-statistics;
            'test="f"':     F-statistics;
            'test="fc"':    fold changes among classes;
            'test="sam"':   SAM-statistics;
            'test="modt"':  moderated t-statistics;
            'test="modf"':  moderated F-statistics;
            'test="B"':     B-statistics.

_D_e_t_a_i_l_s:

     Given the names of the test statistics, 'deds.genExtra' generates
     extra parameters needed to be passed in the functions 'comp.stat'
     and 'deds.stat.linkC' for the assessment of differential
     expression. Both functions are interfaces to C functions.
     'deds.genExtra' generates default parameters as follows: 
      If 'test="t" or "f", "fc", "modt", "modf"', the extra parameter
     needed is the number of classes; 
      If 'test="sam"', the extra parameter needed is the percentile of
     within-gene standard deviations that the fudge factor s_0 will be
     set at and the default is 0.5; 
      If 'test="B"', the extra parameter needed is the percentage of
     alternative hypotheses (differential expression) and the default
     is set at 0.01.

_V_a_l_u_e:

     A numeric vector, the length of which is determined by the length
     of the names of the test statistics for the argument 'test'.

_A_u_t_h_o_r(_s):

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

_S_e_e _A_l_s_o:

     'comp.stat', 'deds.stat.linkC'

_E_x_a_m_p_l_e_s:

     ## two sample test
     L <- rep(0:1, c(5,5))
     extras <- deds.genExtra(L, c("t","sam", "B"))
     ## extras will be c(2, 0.5, 0.01)

