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, array2=0, genesToLabel=NULL, labelCol="red", log=TRUE,labelpch=16,identify=FALSE, 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 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: numeric value specifying what fold change lines to display on
          the plot

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

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

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

     A plot will be produced of the average values for each gene found
     in sample 1 against the averages found in sample 2. 

     If identify is set to TRUE then clicking on each point will
     display information about the ProbeID, gene name and values from
     both samples of the point  clicked

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

     Plot will be produced on the current graphical device

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

     Mark Dunning

