IsoGenemSAM             package:IsoGene             R Documentation

_T_h_e _f_i_v_e _S_A_M _t_e_s_t _s_t_a_t_i_s_t_i_c_s _c_a_l_c_u_l_a_t_e_d _f_o_r _b_o_t_h _t_h_e _i_n_c_r_e_a_s_i_n_g _a_n_d
_d_e_c_r_e_a_s_i_n_g _t_r_e_n_d_s

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

     The function calculates the values for the five SAM test
     statistics (the global likelihood test, Williams, Marcus, M, and
     the modified M) for the most likely direction.

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

     IsoGenemSAM(x, y, fudge.factor)

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

       x: indicates the dose levels

       y: gene expression for all genes

fudge.factor: the fudge factor values to be used in the SAM test
          statistics

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

     A list with components  

      E2: the SAM test statistic of global likelihood test for the
          likely direction of each gene.

Williams: the test statistic of Williams for the likely direction of
          each gene.

 Marcus : the test statistic of Marcus for the likely direction of each
          gene.

      M : the M test statistic for the likely direction of each gene.

   ModM : the test statistic of the modified M for the likely direction
          of each gene.

direction: the direction with the higher likelihood of increasing
          (indicated by "u") or decreasing (indicated by "d") trend.

_N_o_t_e:

     This function calculates the five test statistics for both
     increasing and decreasing ordered alternatives for all the genes
     (rows in the data set).

_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:

     'isoreg', 'IsoGene1', 'Isofudge'

