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, array, n=3,log=FALSE,label=FALSE,main=NULL,ylim=NULL,...)

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

  BLData: BeadLevelList object

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

   array: numeric value giving the array we are interested in

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

     log: if TRUE log2 intensities of each bead are used to find
          outliers

   label: if TRUE all beads will be given a numeric ID on the plot

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

    main: specify a title for the plot

     ...: 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 simply finding the value of BLData$R for each bead in the array
     whose BLData$ProbeID  matches the specified ProbeID. The distance
     from the centre of the hexagon can be found in a similar fashion
     by looking at BLData$x and BLData$y. 

     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)

     #By default, outliers found by Illumina method are highlighted

     plotBeadIntensities(BLData, 2, 1)

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

     plotBeadIntensities(BLData, 2, 1, log=TRUE, n=5)

     #Increasing n selects only the most extreme outliers

     plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=3)

     plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=4.5)

     plotBeadIntensities(BLData, 4279, 1, log=TRUE, n=6)

