BeadSummaryList-class       package:beadarray       R Documentation

_S_t_o_r_e_s _b_e_a_d _s_u_m_m_a_r_y _d_a_t_a - _c_l_a_s_s

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

     A list based class for storing bead summary data. 
     'BeadSummaryList' objects can be created from 'BeadLevelList'
     objects or by reading  directly from pre-processed BeadStudio
     output by using the 'readBeadSummaryData' function.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects should contain the following list components:

       'R':           Numeric matrix containing foreground intensites for the red channel.  Rows correspond to beadtypes and columns to arrays.
       'Rb':          Numeric matrix containing background intensites for the red channel.
       'BeadStDev':   Standard deviations for each bead type per array.
       'NoBeads':     Number of beads of each type per array.
       'ProbeID':     ID for each probe on the arrays.
       'nooutliers':  The number of beads flagged as outliers for each bead type per array. This is only used for bead summary data created by beadarray and not for pre-processed data read from BeadStudio

_M_e_t_h_o_d_s:

     'BeadSummaryLists' can be subsetted and combined.  They also
     return dimensions so functions such as'dim', 'nrow' and 'ncol' are
     also defined.  'BeadSummaryList' uses an adapted version of the
     'show' method from the Limma class 'LargeDataObject'.  This means
     that the 'BeadSummaryList' will print in a relatively compact way.

     Other functions which operate on 'BeadSummaryList' objects
     include: 'plotXY.beads' 'plotMA.beads' 'getMeanIntensities'
     'pairwiseMA'

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

     Mark Dunning and Mike Smith

