probePairsPlot           package:beadarray           R Documentation

_Q_A _p_l_o_t _u_s_i_n_g _p_e_r_f_e_c_t _m_a_t_c_h _a_n_d _m_i_s_m_a_t_c_h _c_o_n_t_r_o_l_s

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

     QA using the hybridisations controls that are identical expect for
     a few bases. Hence lower signal should be observed for the
     mismatch probes.

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

     probePairsPlot(BLData, array = 1)

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

  BLData: A BeadLevelList object for an Illumina expression array

   array: Number of the array in BLData that we want QA for

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

     Firstly, the annotation of the control probes found on the
     BeadLevelList object is retrieved. We then search the annoation
     for the perfect and mismatch controls (labeled
     phage_lambda_genome:pm and phage_lambda_genome:mm2).  For each
     perfect match we find the corresponding mismatch control by
     comparing the sequences and plot the perfect match control next to
     the mismatch control.

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

     Plot on the current graphical device with the perfect match beads
     in red and mismatches in purple. The labels on the x-axis show the
     ID of the controls.

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

     Mark Dunning

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

     'calculateBeadLevelScores'

