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' , 'NChannelSet', 'BeadLevelList', 'RGList', 'MAList',
     'marrayRaw' or 'marrayNorm' 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, grouprep)

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

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

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

expressionset: is an object of class 'ExpressionSet', 'AffyBatch' ,
          'NChannelSet' , 'BeadLevelList' , 'RGList' , 'MAList' ,
          'marrayRaw' or 'marrayNorm' .

  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. 

grouprep: Decide if you want the boxplots and density plots to be
          coloured function of the groups set by 'intgroup'. The
          default is FALSE meaning that the boxplot and density plots
          will not be represented function of the groups of 'intgroup'.

_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)

