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.

     As a result of both having identical function names this function
     can conflict with the 'plotMA' method in 'limma'.  If both
     packages are loaded, the function from whichever package was
     loaded last takes precedence.  If the 'beadarray' plotMA()
     function is masking that from 'limma', one can directly call the
     'limma' method using the command "limma::plotMA()". 
     Alternatively, one can detach the 'beadarray' package using
     "detach(package:beadarray)".  Similar techniques can be used if
     'limma' is masking the 'beadarray' method.

_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)

