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 against their distance from the centre of the array.
     Any outliers for the bead type will be highlighted.

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

     plotBeadIntensities(BLData, ProbeIDs, arrays, log = FALSE, n=3,
               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 for the bead type 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)

       n: outlier values for the bead type are beads with intensity
          more than 'n' times away from the mean

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:

     We find the intensities for each bead of the specified bead type
     by finding the G, Gb, R or Rb intensities for each bead in the
     array whose BLData$ProbeID matches the specified ProbeID. The
     distance from the centre of the hexagon can be found in a similar
     fashion by looking at the GrnX and GrnY values.

     The outliers for the bead type are beads which have intensity more
     than 'n' times away from the standard deviation using logged or
     un-logged bead intensities (specified using 'log' argument).

     The mean for the bead type and lines 3 standard deviations from
     the mean are shown on the plot.

_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)

