plot.single.slide            package:sma            R Documentation

_M _v_s. _A _P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     For a single slide, this function produces a scatter plot of log
     intensity ratios M = log_2(R/G) versus average log intensities A =
     log_2(R*G)/2, where R and G represent the fluorescence intensities
     in the red and green channels respectively, with the addition of
     coloured lines indicating the cutoffs given by each of the three
     single slide methods.

_U_s_a_g_e:

     plot.single.slide(x,layout,norm="p",image.id=1,...)

_A_r_g_u_m_e_n_t_s:

       x: A list with at least 4 elements.  Each element of the list
          being a matrix with p rows for p genes and n columns for n
          slides.  The first element 'R' contains the raw red
          intensities, the second element 'G' contains the raw green
          intensities, the third element 'Rb' contains the background
          red intensities and the 4th element 'Gb' contains the
          background green intensities. This data structure can be
          generated by an interactive function 'init.data'.

  layout: a list specifying the dimensions of the spot matrix and the
          grid matrix.  This can be generated by calling 'init.grid'.

    norm: character string, one of "n", "m", "l", "p" or "s".  This
          argument  specifies the type of normalization method to be
          performed: "n" no normalization between the 2 channels; "m"
          'median' normalization, which sets the median of log
          intensity ratios to zero; "l" global 'lowess' normalization;
          "p" print-tip group lowess normalization and "s" scaled
          print-tip group lowess normalization.

image.id: integer value; the index of the slide which is considered.

     ...: additional graphical parameters

_D_e_t_a_i_l_s:

     Plots an M vs A plot with results from each of the three single
     slide methods, the methods of Newton, Sapir-Churchill and Chen,
     indicated by colored lines. Solid black lines correspond to
     Newtons method at 1:1, 1:10 and 1:100 log odds, note that the
     points are colored red and green depending on where they fall
     according to this method. Dashed lines are Chens method at the 95%
     and 99% confidence levels. Dotted lines are Sapir-Churchil method
     at 95% and 99% posterior probabilites.

_V_a_l_u_e:

     A plot is created on the current graphics device.  The plot is an
     M vs A plot with lines indicating cuttoff for the three single
     slide methods

_A_u_t_h_o_r(_s):

     Ben Bolstad, bolstad@stat.berkeley.edu

_S_e_e _A_l_s_o:

     'stat.Chen', 'stat.ChurSap', 'stat.Chen'

_E_x_a_m_p_l_e_s:

     data(MouseArray)
     # mouse.setup <- init.grid()
     # mouse.data <- init.data() ## see \emph{init.data}
     plot.single.slide(mouse.data, mouse.setup, norm="p", image.id=3)

