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',
     'aqmInputObj', '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, intgroup, grouprep)

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

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

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

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

intgroup: Name of the column of the phenoData to be used to draw a
          colour 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'.

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

     See the arrayQualityMetrics Vignette for examples of this
     function.

_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>

