fudge2               package:siggenes               R Documentation

_F_u_d_g_e _F_a_c_t_o_r

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

     Computes the fudge factor as described by Tusher et al. (2001).

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

       fudge2(r, s, alpha = seq(0, 1, 0.05), include.zero = TRUE)

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

       r: a numeric vector. The numerator of the test statistic
          computed for each gene is represented by one component of
          this vector.

       s: a numeric vector. Each component of this vector corresponds
          to the denominator of the test statistic of a gene.

   alpha: a numeric value or vector specifying quantiles of the 's'
          values. If 'alpha' is numeric, this quantile of 's' will be
          used as fudge factor. Otherwise, the 'alpha' quantile of the
          's' values is computed that is optimal following the
          criterion of Tusher et al. (2001).

include.zero: if 'TRUE', s0=0 is also a possible choice for the fudge
          factor.

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

  s.zero: the value of the fudge factor s0.

alpha.hat: the optimal quantile of the 's' values. If  s0=0,
          'alpha.hat' will not be returned.

  vec.cv: the vector of the coefficients of variations.  Following
          Tusher et al. (2001), the optimal 'alpha' quantile  is given
          by the quantile that leads to the smallest CV of the modified
          test statistics.

     msg: a character string summarizing the most important 
          information about the fudge factor.

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

     Holger Schwender, holger.schw@gmx.de

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

     Tusher, V., Tibshirani, R., and Chu, G. (2001). Significance
     Analysis of Microarrays Applied to the Ionizing Radiation
     Response. _PNAS_, 98, 5116-5121.

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

     'SAM-class','sam'

