calculateBeadLevelScores      package:beadarray      R Documentation

_Q_u_a_l_i_t_y _a_s_s_e_s_s_m_e_n_t _f_o_r _e_x_p_r_e_s_s_i_o_n _c_h_i_p_s

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

     A collection of functions for tabulating and plotting various
     quality control measurements derived from the bead-level data for
     Illumina expression chips. Currently, Humanv1, Humanv2, Humanv3,
     Mousev1, Mousev1p1, Mousev2 and Rat chips are supported.

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

     calculateBeadLevelScores(BLData, path = "QC", log = TRUE, plot = FALSE, 
                              replacePlots=TRUE, writeToFile = TRUE)

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

  BLData: A BeadLeveList for an expression chip. The annotation slot of
          the object should define the type of chip 

    path: Specifies the directory where diagnostics plot are to be
          saved in

     log: (used for outlier calculations) if TRUE calculate outliers on
          the log2 scale.  If FALSE calculate outliers on the original
          scale

    plot: if TRUE then diagnostic plots will be generated

writeToFile: Argument describing whether results of QA assessment
          should be output to html, txt or not output at all

replacePlots: if TRUE any plots that have already been created will be
          replaced

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

     For these QA tools we make use of the controls probes that
     Illumina use on their expression chips to detect the presence, or
     lack of, expression. See <URL:
     www.illumina.com/downloads/GX_QualityControl_TechNote.pdf> for an
     overview of these controls. Illumina provide a means to visualize
     these controls, but the values reported are _after outlier
     removal_ and there is no way to infer how many outliers are
     removed. Therefore, one does not get a true impression of the
     quality of an array. For instance, low intensity observations for
     positive controls may indicate a spatial defect.

     For our QA measurements we perform a detection score calculation
     the same as Illumina, except on per-bead observations for each
     control type rather than the summarized values. Specifically, we
     test each bead observation of a given control bead-type for
     detection by computing a p-value: 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. Another adaptation is to change the
     bead-types used as a reference in the calculation rather than the
     negative controls. For example, there are a series of
     sample-independent controls that have probe sequences
     complementary to oligonucleotides spiked into the hybridization
     solution and hence should always have detectable signal. For some
     of these bead types (six on the Human6 V3), the concentration is
     either "medium", "low" or "high", with the intention that there
     should be a predictable gradient between the controls. Thus, we
     test if the bead-types with a medium concentration are detected
     compared to the low controls and similar for the medium and high
     controls.

     The purpose of calculateBeadLevelScores is to calculate the
     following QA measures for all arrays in the BeadLevelList objects
     and return them in the arrayInfo slot of the BeadLevelList object.
     We also record the number of outliers found on the array.

     If the plot argument to calculateBeadLevelScores is set to TRUE,
     then a number of diagnostic plots will be produced for each and
     compiled into a HTML page for that array. The location of these
     completed pages is specified by the path argument. Finally, if
     writeToFile is set to html, a html page compiling all the QA
     measures for the chip will be created.

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

     A modified version of BeadLevelList is created with the QA
     measures stored in a qcScores slot.

  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.

  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 and Andy Lynch

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

     'outlierPlot', 'lmhPlot', 'poscontPlot', 'backgroundControlPlot'

