oddsplot              package:pickgene              R Documentation

_O_d_d_s _P_l_o_t _f_o_r _D_i_f_f_e_r_e_n_t_i_a_l _M_i_c_r_o_a_r_r_a_y _E_x_p_r_e_s_s_i_o_n

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

     The function plots contours for the odds that points on microarray
     show differential expression between two conditions (e.g. Cy3 and
     Cy5 dye channels on the same microarray).

_U_s_a_g_e:

     oddsplot(x, y, theta, by.level = 10, rotate = FALSE, offset =
              0, main = "", xlab = xlabs, ylab = ylabs, col = NULL,
              cex = c(0.25, 0.75), shrink = FALSE, lims =
              range(c(x, y)))

_A_r_g_u_m_e_n_t_s:

       x: first condition expression levels

       y: second condition expression levels

   theta: four parameters from 'em.ggb'

by.level: odds plot contours increase by this level

  rotate: rotate to average versus ratio if TRUE, otherwise plot
          conditions against each other

  offset: offset for 'log' transform

    main: main title for plot

    xlab: horizontal axis label (default if 'Cy3' if 'rotate' is FALSE,
          'Average Intensity' otherwise

    ylab: vertical axis label (default if 'Cy5' if 'rotate' is FALSE,
          'Cy3 / Cy5' otherwise

     col: color of points (if NULL, use black for non-changing points,
          blue for changing points)

     cex: character expansion (use 'rep(.25,2)' to have all points the
          same size)

  shrink: use shrinkage on expression levels if TRUE (default is FALSE)

    lims: limits for plot area

_D_e_t_a_i_l_s:

     Fit Gamma/Gamma/Bernoulli model (equal marginal distributions) The
     model has spot intensities x ~ Gamma(a,b); y ~ Gamma(a,c). The
     shape parameters b and c are ~ Gamma(a0,nu). With probability p, b
     = c; otherwise b != c. All spots are assumed to be independent.

_V_a_l_u_e:

     Log odds for all points in original order.

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

     Michael Newton

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

     MA Newton, CM Kendziorski, CS Richmond, FR Blattner and KW Tsui
     (2000) ``On differential variability of expression ratios:
     improving statistical inference about gene expression changes from
     microarray data,'' _J Computational Biology 00_: 000-000.

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

     'em.ggb'

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

     ## Not run: 
     oddsplot( x, y )
     ## End(Not run)

