qc                package:simpleaffy                R Documentation

_G_e_n_e_r_a_t_e _Q_C _s_t_a_t_s _f_r_o_m _a_n _A_f_f_y_B_a_t_c_h _o_b_j_e_c_t

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

     Generate QC metrix for Affymetrix data.

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

     qc(unnormalised, ...)

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

unnormalised: An AffyBatch object with nowt done to it 

     ...: Any other parameters 

_D_e_t_a_i_l_s:

     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.

     Before using this function you are strongly encouraged to read the
     'QC and Affymetrix data' document, which contains detailed
     examples.

     This function takes an 'AffyBatch' object and generates a
     'QCStats' object containing a set of QC metrics. See 'qc.affy' for
     more details.

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

     Crispin J Miller

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

     'qc.affy' 'setQCEnvironment'

_E_x_a_m_p_l_e_s:

       ## Not run: 
         qcs <- qc(eset,eset.mas)
       
     ## End(Not run)
       data(qcs)
       ratios(qcs)
       avbg(qcs)
       maxbg(qcs)
       minbg(qcs)
       spikeInProbes(qcs)
       qcProbes(qcs)
       percent.present(qcs)
       plot(qcs)
       sfs(qcs)
       target(qcs)
       ratios(qcs)

