plotMAXY              package:beadarray              R Documentation

_S_c_a_t_t_e_r _p_l_o_t_s _a_n_d _M_A-_p_l_o_t_s _f_o_r _a_l_l _s_p_e_c_i_f_i_e_d _a_r_r_a_y_s

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

     Produces scatter and MA-plots for all pairwise comparisons that
     can be made from a set of arrays.

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

     plotMAXY(exprs, arrays, log = TRUE, genesToLabel=NULL,
              labels=colnames(exprs)[arrays],labelCol="red",
              labelpch=16,foldLine=2,sampleSize=NULL,...)

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

   exprs: an expression matrix from an ExpressionSet or eSet

  arrays: numeric vector giving the indices of the arrays in BSData we
          want to plot

     log: if TRUE then all values will be log2-transformed before
          plotting

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

  labels: vector of array names to display on the plot

labelCol: plotting colours for highlighted genes

labelpch: plotting characters for highlighted genes

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

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

     ...: other graphical parameters to be passed

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

     This graphical tool shows differences that exist between two
     arrays and can be used to highlight biases between arrays as well
     as highlighting genes which are differentially expressed.  For
     each bead type, we take the averaged intensity calculated from two
     different arrays. On an XY plot these values are plotted against
     each other and on the MA plot, log2-ratios is plotted against the
     average intensities.

     In the lower-left section of the plot we see XY plots for all
     pairwise comparisons between the arrays and in the upper right we
     have pairwise MA plots. Going down the first column we observe XY
     plots of array 1 against array 2 and array 1 against array 3 etc.
     Similarly, in the upper-right corner we can observe pairwise MA
     plots.

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

     Mark Dunning

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

     data(BSData)

     vec = c(1,2,3)
     labs = colnames(exprs(BSData))
     plotMAXY(exprs(BSData), vec, labels=labs)

