qc.get.alpha1           package:simpleaffy           R Documentation

_G_e_t _o_r _s_e_t _t_h_e _a_l_p_h_a _v_a_l_u_e_s _f_o_r _t_h_e _c_u_r_r_e_n_t _Q_C _e_n_v_i_r_o_n_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     Alpha1 and Alpha2 are used to define the P/M/A thresholds for
     detection calling algorithm see - 'detection.p.val'. These are
     array dependent, these functions set or get their values. Tau is a
     constant parameter within the calculation and is not array
     specific.

_U_s_a_g_e:

      qc.get.alpha1()
      qc.set.alpha1(value)
      qc.get.alpha2()
      qc.set.alpha2(value)
      qc.get.tau()

_A_r_g_u_m_e_n_t_s:

   value: A double representing the alpha1 or alpha2 threshold for
          defining detection calls. See 'detection.p.val' for more
          details.

_V_a_l_u_e:

     'qc.set.alpha1' and 'qc.set.alpha2' return nothing.
     'qc.get.alpha1' and 'qc.get.alpha2' return a double.

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Crispin J Miller

_R_e_f_e_r_e_n_c_e_s:

     http://bioinformatics.picr.man.ac.uk/

_S_e_e _A_l_s_o:

     'detection.p.val'

_E_x_a_m_p_l_e_s:

       setQCEnvironment("hgu133plus2cdf")
       qc.get.alpha1()
       qc.get.alpha2()
       qc.set.alpha1(0.05)
       qc.get.alpha1()
       qc.set.alpha2(0.05)
       qc.get.alpha2()