plotMA                 package:limma                 R Documentation

_M_A-_P_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Creates an MA-plot with color coding for various sort of control
     spots.

_U_s_a_g_e:

     plotMA(MA,array=1,pch=16,status=NULL,
            values=c("gene","blank","buffer","utility","negative","calibration","ratio"),
            col=c("black","yellow","orange","pink","brown","blue","red"),
            cex=c(0.1,0.6,0.6,0.6,0.6,0.6,0.6))

_A_r_g_u_m_e_n_t_s:

      MA: list with components 'M' containing log-ratios and 'A'
          containing average intensities

   array: integer giving the array to be plotted. Corresponds to
          columns of 'M' and 'A'.

     pch: vector or list of plotting characters

  status: character vector giving the control status of each spot on
          the array. If 'NULL' then subsequent arguments are ignored.

  values: character vector giving unique values of 'status'
          corresponding to control states of interest

     col: vector of colors, of the same length as 'values'

     cex: numeric vector of the same length as 'values' giving sizes
          for plot symbols

_D_e_t_a_i_l_s:

     See 'points' for possible values for 'pch', 'col' and 'cex'.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of diagnostic functions available in LIMMA is given in
     6.Diagnostics.

