poscontPlot            package:beadarray            R Documentation

_P_l_o_t _b_e_a_d-_l_e_v_e_l _h_o_u_s_e_k_e_e_p_i_n_g _a_n_d _b_i_o_t_i_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 biotin and housekeeping
     controls for an expression array. We know these controls should
     show high signal and are therefore useful for QA purposes. The
     housekeeping control targets a bead-type believed to be
     universally expressed whereas the biotin control targets the
     biotin used for staining. By considering all bead observations
     (unlike the plots produced by BeadStudio) we get an detailed
     impression of array quality.

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

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

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

  BLData: A BeadLevelList object for an Illumina expression array

   array: The number of the array of interest

    plot: if TRUE a diagnostic plot will be produced, otherwise only
          summary values are returned.

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

     The IDs for the housekeeping and biotin controls are retrieved
     making use of the annotation information stored for the array. If
     this information is incorrect, or missing, then the function will
     not proceed correctly. Valid names for the annotation slot must
     match the names of the ExpressionControlData object provided with
     beadarray. Assuming the controls can be identified, we then
     perform a detection test for each bead observation by computing a
     p-value: of 1-R/N, where R is the relative rank of the bead
     intensity when compared to the N negative controls. Thus, if a
     particular bead has higher intensity than all the negative
     controls it will be assigned a value of 0. After these p-values
     have been calculated for all replicates of the bead type we report
     the percentage of beads with p-values lower than a set threshold
     of 0.05 (currently in favour in the Illumina literature). The
     percentage of beads that are detected at a set threshold is then
     reported for the housekeeping and biotin controls respecitvely.

     If plot is TRUE, the values of all bead observations are plotted
     for each bead-type respectively grouped together according to the
     type of control (housekeeping or biotin). Any beads with low
     intensity may be due to array defects and would be impossible to
     detect with summarized data only. If available, the intensities of
     any high stringency probes will also be plotted.

     An important point to note that the utility of these housekeeping
     controls is dependant on the probe sequences used targeting the
     intended genes. If a particular housekeeping control shows lower
     expression, then it is worth checking the probe sequence by a BLAT
     search of by checking pre-complied tables from
     http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html.

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

HkpDet - %age of housekeeping control beads that are detected compared to the negative controls.: 

BioDet- %age of  biotin labelling control beads that are detected compared to the negative controls.: 

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

     Mark Dunning and Andy Lynch

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

     www.illumina.com/downloads/GX_QualityControl_TechNote.pdf

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

     'calculateBeadLevelScores','setAnnotation'

