qc.affy              package:simpleaffy              R Documentation

_G_e_n_e_r_a_t_e _A_f_f_y_m_e_t_r_i_x _S_t_y_l_e _Q_C _S_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generate QC data for Affymetrix arrays

_U_s_a_g_e:

     qc.affy(unnormalised,normalised=NULL,tau=0.015,logged=TRUE,
             cdfn=cdfName(unnormalised))

_A_r_g_u_m_e_n_t_s:

unnormalised: An unnormalised raw 'AffyBatch' object to call qc stats
          on 

normalised: The same one, processed using 'justMAS' (contains scale
          factors etc.). If not supplied, then the object gets
          calculated internally. 

     tau: used by detection p value

  logged: True if the data is logged 

    cdfn: The cdf name for the array - can be used to specify a
          different set of probes to the default

_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.

     This function takes an (unnormalised) AffyBatch object, and
     (optionally)  an ExprSet, with MAS expression calls produced by
     'call.exprs' and generates QC metrics. If the MAS calls are not
     supplied these are claculated internally.

_V_a_l_u_e:

     A QCStats object describing the supplied 'AffyBatch'

_A_u_t_h_o_r(_s):

     Crispin J Miller

_E_x_a_m_p_l_e_s:

       ## Not run: 
          qcs <- qc(eset)
       
     ## 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)