lumiQ                  package:lumi                  R Documentation

_Q_u_a_l_i_t_y _c_o_n_t_r_o_l _e_v_a_l_u_a_t_i_o_n _o_f _t_h_e _L_u_m_i_B_a_t_c_h _o_b_j_e_c_t

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

     Quality control evaluation of the LumiBatch object and returns a
     summary of the data

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

     lumiQ(x.lumi, logMode = TRUE, detectionTh = 0.01, verbose = TRUE)

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

  x.lumi: a LumiBatch object 

 logMode: transform as log2 or not (the function can check whether it
          is already log transformed.)

detectionTh: the detection threshold used by 'detectionCall' 

 verbose: a boolean to decide whether to print out some messages 

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

     Quality control of a LumiBatch object includes estimating the mean
     and standard deviation of the chips, detectable probe ratio of
     each chip, sample (chip) relations, detecting outliers of samples
     (chips). The produced QC information is kept in the QC slot of
     LumiBatch class. The summary function will provide a summary of
     the QC information (See example).

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

     a LumiBatch object with QC slot keeping the QC information

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

     Pan Du

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

     'LumiBatch', 'plot,LumiBatch-method'

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

     ## load example data
     data(example.lumi)

     ## Do quality control estimation
     lumi.Q <- lumiQ(example.lumi)

     ## A summary of the QC
     summary(lumi.Q, 'QC')

     ## Plot the results
     ## plot the pairwise sample correlation
     plot(lumi.Q, what='pair')

     ## see more examples in "plot,LumiBatch-method" help documents

