comp.t                 package:DEDS                 R Documentation

_C_o_m_p_u_t_i_n_g _O_n_e _a_n_d _T_w_o _S_a_m_p_l_e _t-_s_t_a_t_i_s_t_i_c _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:

     'comp.t' returns a function of one argument with bindings for 'L',
     'mu', 'var.equal'. This function accepts a microarray data matrix
     as its single argment, when evaluated, computes t statistics for
     each row of the matrix.

_U_s_a_g_e:

     comp.t(L = NULL, mu = 0, var.equal = FALSE)

_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. 

      mu: A number indicating the true value of the mean (or difference
          in means if you are performing a two sample test). 

var.equal: a logical variable indicating whether to treat the two
          variances as being equal. If 'TRUE' then the pooled variance
          is used to estimate the variance otherwise the Welch
          statistic will be calculated. 

_D_e_t_a_i_l_s:

     The function returned by 'comp.t' calculates t statistics for each
     row of the microarary data matrix, given specific class labels.

_V_a_l_u_e:

     'comp.t' returns a function with bindings for 'L', 'mu',
     'var.equal', which calculates and returns of vector of t
     statistics for each row in the data matrix.

_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.FC', 'comp.F'

_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

     # two sample test, unequal variance
     t.fun <- comp.t(L)
     t.X <- t.fun(X)

     # two sample test, equal variance
     t.fun <- comp.t(L, var.equal=TRUE)
     t.X <- t.fun(X)

