arrayQualityMetrics   package:arrayQualityMetrics   R Documentation

_Q_u_a_l_i_t_y _m_e_t_r_i_c_s _o_n _m_i_c_r_o_a_r_r_a_y _e_x_p_e_r_i_m_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     'arrayQualityMetrics' performs quality metrics on 'ExpressionSet',
     'AffyBatch' or 'BeadLevelList' or 'NChannelSet' containing
     microarray data from any platforms, one or two channels. The
     results, presented in a HTML report, are designated to allow the
     user to rapidly assess the quality of a set of arrays.

_U_s_a_g_e:

     ## S4 method for signature 'ExpressionSet':
     arrayQualityMetrics(expressionset, outdir,
     force, do.logtransform, split.plots, intgroup)

     arrayQualityMetrics(expressionset,
                         outdir = getwd(),
                         force = FALSE,
                         do.logtransform = FALSE,
                         split.plots = FALSE,
                         intgroup = "Covariate")

     ## S4 method for signature 'AffyBatch':
     arrayQualityMetrics(expressionset, outdir, force,
     do.logtransform, split.plots, intgroup)
     ## S4 method for signature 'NChannelSet':
     arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots, intgroup)
     ## S4 method for signature 'BeadLevelList':
     arrayQualityMetrics(expressionset, outdir,
     force, do.logtransform, split.plots, intgroup)

_A_r_g_u_m_e_n_t_s:

expressionset: is an object of class 'ExpressionSet', 'AffyBatch' or
          'BeadLevelList' or 'NChannelSet'.

  outdir: is the name of the directory in which the results are
          created. 

   force: if TRUE, 'outdir' will be overwritten if it already exists. 

do.logtransform: If TRUE, the data are log transformed before the
          analysis. 

split.plots: If the number of studied array is more than 50 it is
          adviced to define a number of experiments to represent on the
          density plots. 

intgroup: Name of the column of the phenoData to be used to draw a
          color side bar next to the heatmap. 

_V_a_l_u_e:

     A directory 'outdir' containing a HTML report named QMreport.html
     and all the PNG and PDF plots is created.

_A_u_t_h_o_r(_s):

     Audrey Kauffmann, Wolfgang Huber.  Maintainer: <audrey@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

       ## Not run: 
         library(ALLMLL)
         data(MLL.A)
         arrayQualityMetrics(expressionset = MLL.A,
                             outdir ="MLL",
                             do.logtransform = TRUE,
                             split.plots = 10)
         # "QMreport.html" is a report created in the "MLL" directory
         # on the logarithm expression data of the MLL.A AffyBatch.
         # 10 experiments are represented by density plots.
         
     ## End(Not run)

