findHighestChis          package:beadarray          R Documentation

_F_i_n_d _l_e_a_s_t _r_a_n_d_o_m_l_y _d_i_s_t_r_i_b_u_t_e_d _b_e_a_d_s

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

     Function for finding which bead types on an array are least
     randomly positioned.

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

     findHighestChis(BLData, array, limit = 14)

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

  BLData: an BeadLevelList object containing bead level data

   array: numeric value for which array we want to use

   limit: numeric value which determines the threshold value for the
          chi-statistic.

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

     The $\chi^2$ statistic is defined as:

     \begin{center}

     $\chi^2 = \sum^k_{i=1} (O_i - E_i)^2 / E_i$ \end{center}

     where O and E are vectors of length 8 defining the observed and
     expected number of beads in each section respectively.  This
     provides a means of systematically testing the distribution of
     every bead type on a given array and we can record each bead type
     with a sufficiently high value of $\chi^2$.

     If the value for a particular bead type is found to be greater
     than 'limit' then we add the ProbeID for that bead type to a list
     which we later return.

     Default is to use 14 as the limit as this is the 95th quantile for
     the chi-square distribution in question

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

     numeric vector giving ProbeIDs for all bead types on the array
     which give a chi-statistic > 'limit'

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

     Mark Dunning

_E_x_a_m_p_l_e_s:

     data(BLData)

     ##Default setting is to find all bead types with a chi-statistic greater than 14

     findHighestChis(BLData, 1)

     ##Now find all beads with chi-statistic for their distribution greater than 16

     findHighestChis(BLData, 1, limit=16)

     ##ProbeIDs returned by the function can be examined in more detail

     plotBeadLocations(BLData, ProbeID=278, array=1)

     probeDiagnostics(BLData, 278, 1)

