assessSpikeIn2           package:affycomp           R Documentation

_N_e_w _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:

     assessSpikeIn2(s,method.name=NULL,verbose=TRUE)

     assessSpikeInSD(exprset,method.name=NULL,span=1/3)
     assessLS(exprset,method.name=NULL)
     assessMA2(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.

    span: span used in call to 'loess'.

_D_e_t_a_i_l_s:

     'assessMA2' performs the assessment for the second MA-plot (Figure
     1b), 'assessLS' performs the assessment for signal detection plot
     (Figure 4c), 'assessMA2' also perfomrs assessments used by
     fold-change related  plots (Figures 5c-f). 'assessSpikeInSD' is
     for the standard deviation assessment of Figure 2b.
     'assessSpikeIn2' 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

