deds.chooseTest             package:DEDS             R Documentation

_S_e_l_e_c_t_i_o_n _o_f _t_h_e _M_o_s_t _C_o_m_m_o_n _S_t_a_t_i_s_t_i_c_s _f_o_r _D_i_f_f_e_r_e_n_t_i_a_l _E_x_p_r_e_s_s_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     This function selects a set of functions of common statistics for
     differential expression in microarray data analysis, given
     specific observation class labels. As a default, t-statistics,
     fold change and SAM are selected.

_U_s_a_g_e:

     deds.chooseTest(L = NULL, tests = c("t", "sam", "fc"))

_A_r_g_u_m_e_n_t_s:

       L: A vector of integers corresponding to observation (column)
          class labels. For k classes, the labels must be integers
          between 0 and k-1.

   tests: A character vector specifying the statistics to be used to
          test the null hypothesis of no association between the
          variables and the class labels. For DEDS, there should be
          more than one statistic chosen from the following:

            "t":     t-statistics;
            "f":     F-statistics;
            "fc":    fold changes;
            "sam":   SAM-statistics;
            "modt":  moderated t-statistics;
            "modf":  moderated F-statistics;
            "B":     B-statistics.

_D_e_t_a_i_l_s:

     'deds.chooseTest' can be used together with the function
     'deds.stat'. The user specifies the types of statistics needed for
     subsequent DEDS analysis by the argument 'tests' and the function
     returns accordingly a list the statistics function, which could be
     used for input 'testfun' in the function 'deds.stat'.

_V_a_l_u_e:

     A list of statistics functions specified by the user which could
     be used for input in the function 'deds.stat'.

_A_u_t_h_o_r(_s):

     Yuanyuan Xiao, yxiao@itsa.ucsf.edu, 
      Jean Yee Hwa Yang, jean@biostat.ucsf.edu.

_S_e_e _A_l_s_o:

     'comp.t', 'comp.FC', 'comp.SAM'

_E_x_a_m_p_l_e_s:

     X <- matrix(rnorm(1000,0,0.5), nc=10)
     L <- rep(0:1,c(5,5))

     # genes 1-10 are differentially expressed
     X[1:10,6:10]<-X[1:10,6:10]+1

     # as a default, chooses t, fc and sam
     funcs <- deds.chooseTest(L)
     deds.X <- deds.stat(X, L, testfun=funcs)

     # chooses F statistic, SAM statistic, and moderated F statistic
     L <- rep(0:2, c(3,3,4))
     funcs <- deds.chooseTest(L, tests=c("f", "sam", "modf"))

