backgroundControlPlot       package:beadarray       R Documentation

_Q_A _m_e_a_s_u_r_e_s _b_a_s_e_d _o_n _b_e_a_d-_l_e_v_e_l _n_e_g_a_t_i_v_e _c_o_n_t_r_o_l_s

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

     Function for plotting the bead-level intensities for all the
     negative controls that are placed on an array. Typically there are
     around a thousand of these controls, each replicated 30 times. 
     The sequences used for these controls should not target any part
     of the genome and therefore we should not observe any signal.

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

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

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

  BLData: A BeadLevelList for an Illumina expression chip

   array: The number of the array in BLData that we want QA of.

    plot: if TRUE a diagnostic plot will be produced

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

     For QA, we report the mean and variance of all negative controls
     (of all bead-types) after first removing outiers using a 3 MAD
     cut-off. To retrieve the IDs of the negative controls, we make use
     of the annotation slot stored with the BeadLevelList object. It is
     therefore important that this information is accurate.  A plot of
     all negative control bead-types can also be produced, where each
     bead-type is represented by a vertical line covering the
     inter-quartile range and ordered according to mean intensity. Too
     many high intensity values for the negatives could indicate a poor
     quality array.

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

     The function returns the mean (AveNeg) and variance (VarNeg) of
     all negative control beads and a diagnositc plot if requested.

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

     Mark Dunning and Andy Lynch

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

     'calculateBeadLevelScores'

