EBAM-class             package:siggenes             R Documentation

_C_l_a_s_s _E_B_A_M

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

     This is a class representation for the Empirical Bayes Analysis of
     Microarrays (EBAM) proposed by Efron et al. (2001).

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created using the function 'ebam'.

_S_l_o_t_s:


     '_z': Object of class '"numeric"' representing the  expression
          scores of the genes.

     '_p_o_s_t_e_r_i_o_r': Object of class '"numeric"' representing the
          posterior probabilities of the genes.

     '_p_0': Object of class '"numeric"' specifying the prior probability
          that a gene is not differentially expressed.

     '_l_o_c_a_l': Object of class '"numeric"' consisting of the local FDR
          estimates for the genes.

     '_m_a_t._f_d_r': Object of class '"matrix"' containing general
          statistics such as the number of differentially expressed
          genes and  the estimated FDR for the specified values of
          'delta'.

     '_a_0': Object of class '"numeric"' specifying the used value of the
          fudge factor. If not computed, 'a0' will be set to
          'numeric(0)'.

     '_m_a_t._s_a_m_p': Object of class '"matrix"' containing the permuted
          group labels used in the estimation of the null distribution.
          Each row represents one permutation, each column one
          observation (pair). If no permutation procedure has been
          used, 'mat.samp' will be set to 'matrix(numeric(0))'.

     '_v_e_c._p_o_s': Object of class '"numeric"' consisting of the number of
          positive permuted test scores that are absolutely larger than
          the test score of a particular gene for each gene. If not
          computed 'vec.pos' is set to 'numeric(0)'.

     '_v_e_c._n_e_g': Object of class '"numeric"' consisting of the number of
          negative permuted test scores that are absolutely larger than
          the test score of a particular gene for each gene. If not
          computed 'vec.neg' is set to 'numeric(0)'.

     '_m_s_g': Object of class '"character"' containing information about,
          e.g., the type of analysis. 'msg' is printed when the
          functions 'print' and 'summary' are called.

     '_c_h_i_p': Object of class '"character"' naming the microarray used
          in the analysis. If no information about the chip is
          available, 'chip' will be set to '""'.

_M_e_t_h_o_d_s:


     _p_l_o_t 'signature(object = "EBAM")': Generates a plot of the
          posterior probabilities of the genes for a specified value of
           Delta. For details, see 'help.ebam(plot)'. For the
          arguments, see 'args.ebam(plot)'.

     _p_r_i_n_t 'signature(object = "EBAM)': Prints general information such
          as the number of differentially expressed genes and the
          estimated FDR for several values of Delta. For details, see
          'help.ebam(print)'. Arguments can be listed by
          'args.ebam(print)'. 

     _s_h_o_w 'signature(object = "EBAM")': Shows the output of an EBAM
          analysis.

     _s_u_m_m_a_r_y 'signature(object = "EBAM")': Summarizes the results of an
          EBAM analysis for a specified value of Delta. For details,
          see 'help.ebam(summary)'. For the arguments, see
          'args.ebam(summary)'.

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

     Holger Schwender, holger.schw@gmx.de

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

     Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001).
     Empirical Bayes Analysis of a Microarray Experiment, _JASA_, 96,
     1151-1160.

     Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of
     the Empirical Bayes and the Significance Analysis of Microarrays.
     _Technical Report_, SFB 475, University of Dortmund, Germany.

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

     'ebam', 'find.a0', 'FindA0-class'

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

     ## Not run: 
       # Load the data of Golub et al. (1999) contained in the package multtest.
       data(golub)
       
       # golub.cl contains the class labels.
       golub.cl
       
       # Perform an EBAM analysis for the two class unpaired case assuming
       # unequal variances. Specify the fudge factor a0 by the suggested
       # choice of find.a0
       find.out <- find.a0(golub, golub.cl, rand = 123)
       ebam.out <- ebam(find.out)
       ebam.out
         
       # Obtain the number of differentially
       # expressed genes and the FDR if a gene is called differentially
       # expressed if its posterior probability is larger than 0.8, 0.85,
       # 0.9, 0.95.
       print(ebam.out, c(0.8, 0.85, 0.9, 0.95))
         
       # Generate a plot of the posterior probabilities for delta = 0.9.
       plot(ebam.out, 0.9)
         
       # Obtain the list of genes called differentially expressed if their
       # posterior probability is larger than 0.99, and gene-specific 
       # statistics for these variables such as their z-value and their
       # local FDR.
       summary(ebam.out, 0.9)
     ## End(Not run)

