readQC               package:beadarray               R Documentation

_R_e_a_d _a_n_d _p_l_o_t _I_l_l_u_m_i_n_a _q_u_a_l_i_t_y _c_o_n_t_r_o_l _i_n_f_o_r_m_a_t_i_o_n

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

     Reads the standard format of Illumina quality control information
     and produces diagnostic plots

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

     readQC(file, columns=list(Biotin="AVG.Signal.biotin", cy3_high="AVG.Signal.cy3_hyb_high", cy3_low="AVG.Signal.cy3_hyb_low", cy3_med="AVG.Signal.cy3_hyb_med", gene="AVG.Signal.gene", hs="AVG.Signal.high_stringency_hyb", house="AVG.Signal.housekeeping", labeling="AVG.Signal.labeling", mm="AVG.Signal.low_stringency_hyb_mm2", pm="AVG.Signal.low_stringency_hyb_pm", negative="AVG.Signal.negative"),skip=7,sep=",",header=T)
     plotQC(object,...)

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

    file: name of file containing qc information

 columns: a vector of column names to read from the file

    skip: number of lines of header information to ignore in the file

  header: if TRUE the column names in the file are read

     sep: a character string for the file separator

  object: a ExpressionSetIllumina object containing QC information or
          QC object created by readQC

     ...: extra plotting arguments that can be sent to plotQC

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

     The default options are able to read a file which gives quality
     control information and put in a sensible data structure. The
     quality control files  are generated by BeadStudio and given the
     file name _qc_info.csv by default. 

     The information read is given in a assayData structure with Signal
     (average expression), Var (standard error) and Detection matrices.
     The rows of each matrix are arrays in the experiment and columns 
     are the average value of a particular control type.

     A plot giving a overview of all the control types can be produced
     by using plotQC. We can also plot a particular control using
     singleQCPlot and specify whether to plot  the average, standard
     deviation or detection.

_V_a_l_u_e:

     readQC produces an assayData object with Signal, Var and Detection
     matrices

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

     Mark Dunning

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

     data(QC)

     QC$Signal

     data(BSData)

     QC = QCInfo(BSData)

