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 to show an MA plot between two specified samples given by
     different SAMs or the red and green channels of the same sample.

     If two array indices are given then the MA plot will be between
     the two arrays, otherwise the two channels of one array will be
     plotted.

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

     plotMA(exprs, array1, array2=0, genesToLabel=NULL, labelCol="red", foldLine=2,log=TRUE, labelpch=16,identify=FALSE, ma.ylim=2,sampleSize=NULL,...)

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

   exprs: expression matrix from an ExpressionSet or eSet

  array1: numeric value to specify the first sample to be plotted

  array2: numeric value to specify the second sample to be plotted
          (optional)

genesToLabel: vector of gene names to highlight on the plot. These must
          match the rownames of exprs

labelCol: vector of characters to plot for the selected genes

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

labelpch: if TRUE then a log2 transformation will be applied to the
          data before plotting

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

identify: if TRUE, clicking on points on the plot will bring up extra
          information

sampleSize: numeric specifiying the size of a random sample to be taken
          rather than plotting every gene

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

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

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

     In the usual way, M is labelled on the y axis and represents the
     difference between two genes in different samples where as A is
     the average of the two samples.

     Control information must be supplied in a controlTypes vector
     beforehand.

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

     MA plot is displayed on current graphical device.

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

     Mark Dunning

