lmhPlot              package:beadarray              R Documentation

_P_l_o_t _t_h_e _b_e_a_d-_l_e_v_e_l _h_y_b_r_i_d_i_s_a_t_i_o_n _c_o_n_t_r_o_l_s

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

     Function for retrieving and plotting the hybridisation controls
     for an expression array. We know these controls should show high
     signal and are therefore useful for QA purposes. Moreover, we
     should expect to see a gradient between the low, medium and high
     controls. By considering all bead observations (unlike the plots
     produced by BeadStudio) we get an detailed impression of array
     quality.

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

     lmhPlot(BLData, array = 1, plot = FALSE)

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

  BLData: BeadLevelList object for an Illumina expression array which
          must have the annotation slot set appropriately.

   array: The number of the array of interest

    plot: If TRUE then a diagnostic plot will be produced, other only
          summary values will be returned.

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

     The annotation stored with the BLData object in the annotation is
     used to find the IDs of the hybridisation controls. We try and
     find these controls among the bead-level data for the array. If
     not all the control IDs can be found, then the wrong annotation
     may be stored for the array and the function will report an error.
     If found, we test the replicates of the low, medium and high
     controls for detection using the same criteria as used by Illumina
     (implemented in the 'calculateDetection' function). However, an
     important difference is that we test each bead observation
     individually and report for each bead-type the percentage of beads
     detected.

     The function returns five measures that can be used to evaluate
     the quality of the array (see below). On a good quality array, we
     would expect to see 100% for all these measures and a drop from
     100% could indicate a defect on the array. However, it should be
     noted that the HvsM percentage could drop below 100% often due to
     the saturation effect often observed at high intensity. 

     If a plot is requested, the intensities of the hybridisation
     controls are plotted on a y-axis and grouped according to
     different control-type (low, medium or high concentration) on the
     x-axis. Some arrays may have more than one bead-type for a
     particular control.

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

  LowDet: %age of ``low'' control beads that are detected compared to
          the negative controls.

  MedDet: %age of ``medium'' control beads that are detected compared
          to the negative controls.

 HighDet: %age of ``high'' control beads that are detected compared to
          the negative controls.

    MvsL: %age of ``medium'' control beads that are detected compared
          to the ``low'' controls.

    HvsM: %age of ``high'' control beads that are detected compared to
          the ``medium'' controls.

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

     Mark Dunning

_R_e_f_e_r_e_n_c_e_s:

     see <URL:
     www.illumina.com/downloads/GX_QualityControl_TechNote.pdf> for
     description of the hybridisation controls

_S_e_e _A_l_s_o:

     'calculateBeadLevelScores', 'setAnnotation', 'calculateDetection'

