stat.t2                 package:sma                 R Documentation

_T_w_o-_s_a_m_p_l_e _t-_s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Computes two-sample t-statistics for each gene in a multi-slide
     microarray experiment.

_U_s_a_g_e:

     stat.t2(X, cl, x.ratio=FALSE, var.equal=TRUE, ...)

_A_r_g_u_m_e_n_t_s:

       X: if x.ratio=F, X is a list containing two components.  The
          first component is a matrix of log intensity ratios M=log_2
          (R/G) and the second component is the  average log
          intensities A = log_2(R*G)/2, such as the output  from
          'stat.ma'. If x.ratio=T, X is a matrix of log expression
          ratios only.   The rows of X correspond to genes and  columns
          correspond to different hybridizations, that is different
          slides.

      cl: vector of class labels. Must consist of integers 1 and 2.

 x.ratio: logical flag: if TRUE, the matrix X contains only log
          intensity ratios, if FALSE, X is a list containing two
          components.  The first component is a matrix of log
          expression ratios and the second component contains average
          log intensities A.

var.equal: logical flag: if TRUE, the variances of the class 1 and
          class 2 parent populations are assumed equal.

     ...: other parameters used in 't.test'. 

_V_a_l_u_e:

     List containing the following components

       t: the two-sample t-statistic for each gene;

    Num : the numerator of the t-statistic for each gene, with names
          attribute "Num";

Denominator: the denominator of the t-statistic for each gene, with
          names attribute "Den";

      n1: number of class 1 observations used to calculate the
          t-statistic for each gene;

      n2: number of class 2 observations used to calculate the
          t-statistics for each gene;

Average A: if x.ratio=F, the average across all hybridizations of A =
          log_2(R*G)/2,  with names attribute "A.bar", if x.ratio=T,
          NULL is returned.

_N_o_t_e:

     't2stat.func' is called by 'stat.t2' and is not typically used on
     its own.

_A_u_t_h_o_r(_s):

     Sandrine Dudoit, sandrine@stat.berkeley.edu 
      Yee Hwa Yang, yeehwa@stat.berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

     D. Freedman, R. Pisani, and R. Purves. (1998). Statistics, 3rd ed.
     NewYork: W.W. Norton.

_S_e_e _A_l_s_o:

     't2stat.func', 'plot.t2', 'plot.qq', 't.test'.

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     ## mouse.setup <- init.grid()
     ## mouse.data <- init.data() ## see \emph{init.data}
     ## mouse.lratio <- stat.ma(mouse.data, mouse.setup)
     cl <- c(rep(1,3), rep(2,3))
     mouse.t2 <- stat.t2(mouse.lratio, cl)

