IsoBHPlot              package:IsoGene              R Documentation

_P_l_o_t _o_f _a_d_j_u_s_t_e_d _p-_v_a_l_u_e_s _u_s_i_n_g _B_H _o_r _B_Y _a_d_j_u_s_t_m_e_n_t

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

     The function produces a plot with adjusted p-values using BH
     (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutilie
     2004) procedures controlling for FDR. The raw p-values and
     adjusted BH and BY p-values are  plotted.

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

     IsoBHPlot(rp, FDR, stat = c("E2", "Williams", "Marcus",
     "M", "ModifM"))

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

      rp: raw p-value matrix with each row for one gene and 6 columns,
          the first column contains the Probe.ID, the second to the
          sixth columns are raw p-values for the five test statistics

     FDR: the desired FDR to control

    stat: choose one of the five test statistic to use

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

     A plot of adjusted p-values using BH and BY procedures will be
     produced.

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

     Lin et al.

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

     Testing for Trend in Dose-Response Microarray Experiments: a
     Comparison of Testing Procedures, Multiplicity, and
     Resampling-Based Inference, Lin et al. 2007, Stat. App. in Gen. &
     Mol. Bio., 6(1), article 26.

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

     'IsoTestBH',  'IsoRawp'

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

       rp <- data.frame(paste("g", 1:100), matrix(runif(500,0,1), 100, 5))
       IsoBHPlot(rp, FDR = 0.05, stat = "E2")

