spikeInProbes           package:simpleaffy           R Documentation

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

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

     Affymetrix recommend a series of QC metrics that should be used to
     check that arrays have hybridised correctly and that sample
     quality is acceptable. These are discussed in the document 'QC and
     Affymetrix data' accompanying this package, and on the web at
     http://bioinformatics.picr.man.ac.uk. They are described in detail
     in the 'Expression Analysis Fundamentals' manual available from
     Affymetrix.

     Each of these functions queries a QCStats object to retrieve one
     of these QC metrics. Refer to the accompanying documentation for
     more details about the meaning of these values.

     Briefly:

     spikeInProbes:   Returns a table of intensities for the BioB,
     BioC, BioD and CreX probesets. qcProbes:        Returns a table of
     intensities for GAPDH and BetaActin 3', 5' and Mid' probesets.
     avbg:            Returns a vector of the average background levels
     for each array. maxbg:           Returns a vector of the maximum
     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). target:          The target intensity the arrays were
     scaled to. ratios:          A table of 3'/5' and 3'/M' ratios for
     GAPDH and beta-actin

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

     spikeInProbes(object)
     qcProbes(object)
     avbg(object)
     maxbg(object)
     minbg(object)
     percent.present(object)
     sfs(object)
     target(object)
     ratios(object)

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

  object: the QCStats object you want to access 

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

     Crispin J Miller

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

     'qc'

