moreSpikeInProbes          package:yaqcaffy          R Documentation

_A_c_c_e_s_s_o_r _M_e_t_h_o_d_s _f_o_r _Y_A_Q_C_S_t_a_t_s _c_l_a_s_s

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

     The Microarray Quality Control Consortium guidelines and reference
     datasets  are applied to analyse some of the QC metrics
     recommended by Affymetrix.  These guidelines, datasets and QC
     metrics are discussed in detail in the  package vignette. 

     Each of these functions queries a YAQCStats object to retrieve one
     of these QC metrics. The YAQCStats class is a subclass of the
     QCStats object  as defined in the 'simpleaffy' package. 'sfs', 
     'avbg' and 'percent.present' methods access to the
     'scale.factors',  'average.background' and 'percent.present'
     attributes respectivley  are defined in the superclass.

     Briefly:

     isLog:             Returns a logical saying if the expression
     intensities are in log2 from. target:            Returns the
     target value (for MAS 5.0 normalization). moreSpikeInProbes:
     Returns a table of intensities for the internal spike probes.
     gcosProbes:        Returns a table of intensities for GAPDH and
     beta-actin probes. avbg:              Returns a vector of the
     average background levels for each array. minbg:            
     Returns a vector of the minimum background levels for each array.
     percent.present:   Returns a vector listing the percentage of
     probesets called present on each array. sfs:               Returns
     a vector of scale factors for each array (as produced by the MAS
     5.0 algorithm). bioCalls:          Returns a table of
     Present/Marginal/Absent calls for the spike probes. arrays:       
         Returns the names of the arrays in the YAQCStats object. plot:
                  Plots the YACQStats object (see 'yaqc' for more
     details).

_U_s_a_g_e:

     isLog(object)
     avns(object)
     moreSpikeInProbes(object)
     gcosProbes(object)
     bioCalls(object)

_A_r_g_u_m_e_n_t_s:

  object: an object of class '"YAQCStats"'

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

     Laurnet Gatto

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

     'yaqc', 'QCStats'

