Zscore               package:metaArray               R Documentation

_M_e_t_a-_a_n_a_l_y_s_i_s _o_f _M_i_c_r_o_a_r_r_a_y _D_a_t_a _f_r_o_m _D_i_f_f_e_r_e_n_t _P_l_a_t_f_o_r_m_s

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

     This function calculates Z-score for each matched gene across all
     datasets.  In each dataset, it performs local regression smoothing
     of mean vs variance. Z score is constructed by taking the ratio of
     weighted mean difference and  combined standard deviation
     according to Box and Tiao (1992).

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

       Zscore(merged, pheno = NULL, permute = 0, verbose = TRUE)

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

  merged: 'mergeExprSet' object that contains gene expression and class
          label with all datasets. Class label should consist of two
          unique elements. If pheno is NULL, first columns of phenoData
          from each 'ExpressionSet' is sought as class labels. If a
          vector of particular column number in each data is specified,
          corresponding columns of phenoData will be considered for
          class labels.

   pheno: A numeric vector specifying the location of class labels in
          phenoData from each  'ExpressionSet', a unit of
          'mergeExprSet' representing one dataset.

 permute: If permute is 0, weighted Z-score will be referenced to
          standard normal distribution for two-sided p-value.
          Otherwise, columns of all datasets (each dataset separately)
          will be  shuffled at random, from which a permutation
          distribution of Z-scores are formed and Z-scores are 
          referenced to this distribution.

 verbose: If verbose is TRUE, the progress of permutation will be
          reported.

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

     A data.frame with matched genes, Z-scores and p-values will
     result.

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

     Debashis Ghosh <ghoshd@umich.edu>, Hyungwon Choi
     <hwchoi@umich.edu>

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

     J.Wang et al, Bioinformatics 2004 Nov 22;20(17):3166-78

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

      # Zscore(merged, pheno=NULL, permute=10000, verbose=FALSE)

