probeDiagnostics          package:beadarray          R Documentation

_D_i_a_g_n_o_s_t_i_c_s _p_l_o_t _f_o_r _a _b_e_a_d _t_y_p_e

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

     Function to produce 4 diagnostic plots on the same page for a
     particular bead type on an array

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

     probeDiagnostics(BLData, probe, array, label = TRUE,
     log = FALSE, n = 3, showOutliers = TRUE, ...)

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

  BLData: BeadLevelList object

   probe: numeric value giving the ProbeID of the bead type we want to
          plot

   array: numeric value of the array we want

   label: if TRUE all beads will be assigned a numeric label

     log: if TRUE outliers for this bead type will be calculated using
          log2 bead intensities

       n: outliers for this bead type are beads with intensities more
          than 'n' standard deviations from the mean

showOutliers: boolean specifying whether the outliers should be shown
          on the plots

     ...: further graphical parameters to 'plot'

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

     Combines the results of 4 seperate plotting functions onto the
     same page

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

     Plot is produced on the current graphical device.

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

     Mark Dunning

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

     data(BLData)

     probeDiagnostics(BLData, 2, 1)

     probeDiagnostics(BLData, 2, 1, log=TRUE)

     probeDiagnostics(BLData, 2, 1, log=TRUE, label=FALSE)

