assessSpikeIn            package:affycomp            R Documentation

_A_s_s_e_s_s_m_e_n_t _f_u_n_c_t_i_o_n_s _f_o_r _S_p_i_k_e _I_n _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     These functions are assessment functoions. Each takes an
     'exprSet-class' and returns a list with necessary information to
     create assessment plots.

_U_s_a_g_e:

     assessSpikeIn(s,method.name=NULL,verbose=TRUE)

     assessMA(exprset,method.name=NULL)
     assessSignal(exprset,method.name=NULL)
     assessFC(exprset,method.name=NULL)
     assessFC2(exprset,method.name=NULL)

_A_r_g_u_m_e_n_t_s:

       s: An 'exprSet-class' containing exrpession measures for 
          Affymetrix's spike-in experiment.

 exprset: An 'exprSet-class' containing exrpession measures for 
          Affymetrix's spike-in experiment.

method.name: Name of expression measure being assessed.

 verbose: logical. If 'TRUE' show messages.

_D_e_t_a_i_l_s:

     'assessMA' performs the assessment for the MA-plot (Figure 1),
     'assessSignal' performs the assessment for signal detection plot
     (Figure 4a), 'assessFC' perfomrs assessments used by fold-change
     related  plots (Figures 5a, 6a, 6b). 'assessFC2' is for the ROC
     for genes with nominal fold changes of 2 (Figure 5b).
     'assessSpikeIn' is a wrapper for all these and returns a list of
     lists.

_V_a_l_u_e:

     Lists with the necessary information to make the Figures.

_A_u_t_h_o_r(_s):

     Rafael A. Irizarry

