plotXY               package:beadarray               R Documentation

_X_Y _p_l_o_t_s _f_o_r _t_w_o _s_a_m_p_l_e_s

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

     Function to display an XY plot of the average values of genes from
     two different samples or from two channels from the same array.

     If two array indices are given as parameters then two arrays will
     be compared, otherwise the red and green channels from one array
     will be plotted

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

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

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

   exprs: expression matrix from an ExpressionSet or eSet object

  array1: numeric value for the first sample to be plotted

  array2: numeric value for the second sample to be plotted

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

labelCol: plotting colours for highlighted genes

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

labelpch: plotting characters for highlighted genes

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

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:

     Plots the 'array1' intensity versus the 'array2' intensity for
     each gene.

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

     Plot will be produced on the current graphical device

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

     Mark Dunning

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

     data(BSData)

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

