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

