plotMA               package:beadarray               R Documentation

_S_h_o_w _M_A _p_l_o_t_s

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

     Function which produces an MA plot between two specified arrays.

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

     plotMA(exprs, array1=1, array2=2, genesToLabel=NULL, labelCol="red", foldLine=2, log=TRUE, labelpch=16, ma.ylim=2, sampleSize=NULL,...)

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

   exprs: a matrix of expression values

  array1: integer specifying the first array to plot

  array2: integer specifying the second array to plot

genesToLabel: vector of genes to highlight on the plot.  These must
          match the rownames of 'exprs'.

labelCol: plotting colours for highlighted genes

foldLine: a numeric value defining where to draw horizontal fold-change
          lines on the plot

     log: if TRUE the data will be log-transformed before plotting

labelpch: plotting characters for highlighted genes

 ma.ylim: numeric value specifying the range of the plot (from -ma.ylim
          to ma.ylim)

sampleSize: The number of genes to plot.  Default is NULL, which plots
          every gene.

     ...: other graphical parameters to plot that can be specified

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

     The log2 difference in intensity (M-value, log-ratio) are plotted
     against the log2 average intensity (A-value) for each probe for
     the two arrays selected.

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

     A smoothed MA scatter plot is displayed on the current graphical
     device.

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

     Mark Dunning

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

     data(BSData)

     plotMA(exprs(BSData), array1=1, array2=2)

