QCStats-class           package:simpleaffy           R Documentation

_C_l_a_s_s "_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 'qc(AffyBatch)'.

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

     '_s_c_a_l_e._f_a_c_t_o_r_s': Object of class '"numeric"' Scale factors used to
          scale the chips to the specified target intensity 

     '_t_a_r_g_e_t': Object of class '"numeric"' The target intensity to
          which the chips were scaled 

     '_p_e_r_c_e_n_t._p_r_e_s_e_n_t': Object of class '"numeric"' Number of genes
          called present 

     '_a_v_e_r_a_g_e._b_a_c_k_g_r_o_u_n_d': Object of class '"numeric"' The average
          background for the arrays 

     '_m_i_n_i_m_u_m._b_a_c_k_g_r_o_u_n_d': Object of class '"numeric"' The minimum
          background for the arrays 

     '_m_a_x_i_m_u_m._b_a_c_k_g_r_o_u_n_d': Object of class '"numeric"' The maximum
          background for the arrays 

     '_s_p_i_k_e_s': Object of class '"list"' spiked in probes (e.g. biob,
          bioc...) 

     '_q_c._p_r_o_b_e_s': Object of class '"list"' qc probes (e.g. gapdh
          3,5,M,...) 

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

     _a_v_b_g 'signature(object = "QCStats")':  average background

     _m_a_x_b_g 'signature(object = "QCStats")': maximum background 

     _m_i_n_b_g 'signature(object = "QCStats")': minimum background 

     _s_p_i_k_e_I_n_P_r_o_b_e_s 'signature(object = "QCStats")': the spike-in QC
          probes 

     _q_c_P_r_o_b_e_s 'signature(object = "QCStats")': the gapdh and actin QC
          probes 

     _p_e_r_c_e_n_t._p_r_e_s_e_n_t 'signature(object = "QCStats")': no probesets
          called present 

     _p_l_o_t 'signature(x = "QCStats")': Plot a QCStats object 

     _s_f_s 'signature(object = "QCStats")': scale factors 

     _t_a_r_g_e_t 'signature(object = "QCStats")': target scaling 

     _r_a_t_i_o_s 'signature(object = "QCStats")': 5'3' and 5'M ratios for QC
          Probes 

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

     Crispin J Miller

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

