gt.multtest            package:globaltest            R Documentation

_C_o_r_r_e_c_t _g_l_o_b_a_l_t_e_s_t _r_e_s_u_l_t_s _f_o_r _m_u_l_t_i_p_l_e _t_e_s_t_i_n_g

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

     Corrects the raw p-values resulting from a call to 'globaltest'
     for multiple testing, using either Benjamini and Hochberg's False
     Discovery Rate or Holm's procedure for controlling the Family-Wise
     Error Rate.

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

     gt.multtest(gt, proc = c("FDR", "FWER"))

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

      gt: The output of a call to 'globaltest'.

    proc: The procedure to be used. Either "FDR" for Benjamini and
          Hochberg's (1995) False Discovery Rate-controlling procedure
          or "FWER" for Holm's (1979) Family-Wise Error Rate
          controlling procedure.

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

     This function is completely based on the 'mt.rawp2adjp' function
     from the 'multtest' package.

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

     An object of class 'gt.result'.

_N_o_t_e:

     This function must be called _prior_ to any selection of
     significant genes.

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

     Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

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

     For references, type: citation("globaltest"). See also the
     vignette GlobalTest.pdf included with this package.

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

     'globaltest', 'gtGO'.

_E_x_a_m_p_l_e_s:

         # Breast cancer data (ExpressionSet) from the Netherlands Cancer
         # Institute with annotation:
         data(vandeVijver)
         data(annotation.vandeVijver)

         gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)
         sort(gt.multtest(gt))

