plot.t2                 package:sma                 R Documentation

_D_i_a_g_n_o_s_t_i_c _P_l_o_t_s _f_o_r _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:

     Plots of two-sample t-statistics, |t-numerator| and t-denominator
     against average A, and plot of |t-numerator| against
     t-denominator. For each spot on a given slide, A = log_2(R*G)/2,
     where (R,G) denotes the red and green fluorescence intensity pair.
     Points with t-statistics exceeding user defined thresholds are
     highlighted.

_U_s_a_g_e:

     plot.t2(x, main.title="T plots", low=-5, high=5,...)

_A_r_g_u_m_e_n_t_s:

       x: output from the function 'stat.t2'.

main.title: title for the plot.

     low: lower threshold for t-statistic: points with t<low are
          colored in green.

    high: upper threshold for t-statistic: points with t>high are
          colored in red.

     ...: additional graphical parameters

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'stat.t2', 't2stat.func', 'plot', '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)

     ## Calculation of t-statistics
     ## cl <- c(rep(1,3), rep(2,3))
     ## mouse.t2 <- stat.t2(mouse.lratio, cl)

     ## Diagnostic plots
     plot.t2(mouse.t2, "Mouse")

