YAQCStats-class           package:yaqcaffy           R Documentation

_C_l_a_s_s "_Y_A_Q_C_S_t_a_t_s"

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

     Holds Quality Control data for a set of Affymetrix arrays

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'yaqc(object)' where
     object  is of class 'AffyBatch' of 'ExpressionSet'.  YAQCStats is
     a subclass of 'QCStats' and uses the 'scale.factor', 
     'average.background' and 'percent.present', 'arraytype'  and
     'target' attributes of it's subclass.

_S_l_o_t_s:


     '_l_o_g': Object of class '"logical"' that specifies if expression
          values are in log2 form

     '_a_v_e_r_a_g_e._n_o_i_s_e': Object of class '"numeric"' The average noise for
          the arrays 

     '_m_o_r_e_s_p_i_k_e_s': Object of class '"matrix"' More spiked in probes
          (e.g. r2biob5, r2biob3,...) 

     '_g_c_o_s._p_r_o_b_e_s': Object of class '"matrix"' GAPDH and beta-actin qc
          probes  (e.g. gapdh 3,5,M,...) containing the GCOS values

     '_b_i_o._c_a_l_l_s': Object of class '"matrix"' BioB 5',3',M and BioC,
          BioC 5',3'  present/absent/marginal calls 

_M_e_t_h_o_d_s:


     _i_s_L_o_g 'signature(object = "YAQCStats")': are intensities in log2
          form

     _a_v_n_s 'signature(object = "YAQCStats")': average noise

     _m_o_r_e_S_p_i_k_e_I_n_P_r_o_b_e_s 'signature(object = "YAQCStats")': more spike-in
          probes 

     _g_c_o_s_P_r_o_b_e_s 'signature(object = "YAQCStats")': GCOS values of gapdh
          and actin QC probes 

     _b_i_o_C_a_l_l_s 'signature(object = "YAQCStats")': P/M/A calls for BioB,
          BioC and BioD spikes  

     _a_r_r_a_y_s 'signature(object = "YAQCStats")': shows the array names
          composing the 'YAQCStats' object 

     _p_l_o_t 'signature(object = "YAQCStats")': visual representation of
          the qc metrics 

     _s_u_m_m_a_r_y 'signature(object = "YAQCStats")': data frame summary of
          the outliers 

     _s_h_o_w 'signature(object = "YAQCStats")': displays the content of
          the object as a data frame 

     _m_e_r_g_e 'signature(object = "YAQCStats")': merges two compatible
          YAQCStats objects, i.e. that have the same values for the
          'log', 'target' and 'arraytype' slots. 

     _a_r_r_a_y_s 'signature(object = "YAQCStats")': show the array names of
          an YAQCStats objects. 

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

     Laurent Gatto

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

     QCStats-class

