plotBeadIntensities        package:beadarray        R Documentation

_P_l_o_t _b_e_a_d _i_n_t_e_n_s_i_t_i_e_s

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

     Function to plot the intensities of all beads of a particular type
     on an array.

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

     plotBeadIntensities(BLData, ProbeIDs, arrays, log = FALSE,
               whatToPlot="G", ProbeCols=NULL, ylim=NULL,...)

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

  BLData: a BeadLevelList object

ProbeIDs: numeric value giving the ProbeID(s) for the bead type(s) we
          are interested in

  arrays: numeric value giving the array we are interested in

     log: if TRUE log2 intensities are plotted (and used to find
          outliers)

whatToPlot: character string specifying which intensities to plot.
          Possibilities are '"G"', '"Gb"' for single channel data and
          '"G"', '"Gb"', '"R"' and '"Rb"' for two-colour data

ProbeCols: vector of colour names to assign to each bead type

    ylim: vector providing the upper and lower bounds for the y-axis in
          the plotting window

     ...: further graphical parameters to 'plot'

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

     Boxplots of the G, Gb, R or Rb intensities on the original or
     log-scale for each bead type specified by 'ProbeIDs' on selected
     'arrays' is produced.

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

     Plot is produced on current graphical device

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

     Mark Dunning

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

     data(BLData)

     plotBeadIntensities(BLData, arrays=seq(1:4), ProbeIDs=c(2,1000), log=TRUE)

