MAplotPara             package:affyPara             R Documentation

_P_a_r_a_l_l_e_l_i_z_e_d _r_e_l_a_t_i_v_e _M _v_s. _A _p_l_o_t_s _f_o_r _M_i_c_r_o_a_r_r_a_y _D_a_t_a

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

     Parallelized creation of M vs A plots. Where M is determined
     relative to a specified chip or to a pseudo-median reference chip.
     And optimized plots for a large number of microarrays.

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

     MAplotPara(object, 
                            log=TRUE, 
                            type=c("both","pm","mm"),
                            ref=NULL,
                            which=NULL, 
                            ref.title="vs mean ref.Array",
                            subset=NULL,
                            span=1/4,
                            show.statistics=TRUE,
                            family.loess ="gaussian", 
                            pch=".",
                            plot =TRUE,
                            cutoff =0.5,# add parameter to generic function ma.plot
                            level=1,
                            cluster, verbose = getOption("verbose"),
                            ... )
                            

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

  object: An object of class AffyBatch  OR a 'character' vector with
          the names of CEL files  OR a (partitioned) list of
          'character' vectors with CEL file names.

     ...: Additional parameters for the routine.

     log: A logical value. TRUE as default. Computes logarithms of
          Array's intensities.

    type: Defines how the Affimetrix Array's intensities should be
          considered  (only for Affymetrix: perfect match(pm), mismatch
          or both).

     ref: gives the possibility to define some array of the Affybatch
          object as 'medianchip'  otherwise it will be calculate as
          reference median array.

   which: A list of index samples from the object class, which
          indicates the samples to be ploted.

ref.title: character- gives a 'title' to label the plots by ma.plot
          function.

  subset: A set of indices to use when drawing the loess curve.

    span: span to be used for loess fit.

family.loess: '"guassian"' or '"symmetric"' as in loess.

show.statistics: A logical value. TRUE as default.  If true some
          summary statistics of the M values are drawn.

     pch: Graphical plotting 'character'. Default Value '"."'
          equivalently to 'pch = 46'  from the function points 

    plot: A logical value. TRUE as default, MAplots will be drawn
          otherwise only the "bad" quality arrays will be calculated.

  cutoff: numerical between [0.0-1.0]. As default 0.5. It is considered
          as limit for the sigma parameter,  which is one of the three
          classificators for the 'bad' quality arrays by MAplotsPara.

   level: level- numerical - indicates which level of "bad" quality
          arrays should be plot if plotDraw =TRUE: 1 - only first level
          "bad" quality  will be considered. First level "bad" array
          quality are the arrays considered as "bad" after the three
          possible parameter: S, loess, and sigma  2 - first level 
          "bad" quality and second level  will be considered. Second
          level "bad" quality Arrays are the arrays which has been
          classified as bad after two of the three possible parameter 
          3 - all levels will be plot : first, second and third. Third
          level "bad" quality Arrays are the arrays which are
          considered as "bad" after one of the three parameter. 

 cluster: A cluster object obtained from the function makeCluster in
          the SNOW package.  For default '.affyParaInternalEnv$cl' 
          will be used. 

 verbose: A logical value. If 'TRUE' it writes out some messages.
          default: getOption("verbose") 

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

     MAplotPara is a function based on the generic function ma.plot
     from affy package. Only the following parameters are original for
     MAplotPAra: cluster, object, cuttof, plot, level The parameter
     ref.fn=c("median","mean") is not allowed because it is not
     possible to calculate the reference median array as parallelized.

     'MAplotPara' is the parallelized function for MA plots of probe
     intensities.  It is a function to check and control the Data
     quality of the samples using the MA plot method.  For serial
     function an more details see boxplot. This function is optimized
     for huge numbers of microarray data.

     For using this function a computer cluster using the SNOW package
     has to be started.  Starting the cluster with the command
     'makeCluster' generates an cluster object in the affyPara
     environment (.affyParaInternalEnv) and  no cluster object in the
     global environment. The cluster object in the affyPara environment
     will be used as default cluster object,  therefore no more cluster
     object handling is required.   The 'makeXXXcluster' functions from
     the package SNOW can be used to create an cluster object in the
     global environment and  to use it for the preprocessing functions.

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

     MAplotPara return a list with four elements: 'values_MAP',
     'loess_y', 'quality_MAP', 'results_MAP'. 

values_MAP: is a matrix which contains the calculated values for all
          arrays of the object ('sampleNames', 'S', 'osc_Loess',
          'sigma', 'var_sigma').

 loess_y: contains the y values (50 points) of the loess curve, which
          are used to calculate the 'osc_Loess' from 'values_MAP'

quality_MAP: list which contains all "bad" quality Arrays

results_MAP: summary from 'quality_MAP' as matrix, which contains only
          the Arrays that are considered as "bad" quality and in which
          levels are they classified. Possible values are 0 if the
          Array is not at this levels and 1 if it is classified as
          "bad" sample at this level.

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

     Esmeralda Vicedo <e.vicedo@gmx.net>, Markus Schmidberger
     schmidb@ibe.med.uni-muenchen.de, Ulrich Mansmann
     mansmann@ibe.med.uni-muenchen.de

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

     ## Not run: 
     library(affyPara)
     if (require(affydata)) {
       data(Dilution)

       makeCluster(3)

       ##MA of Dilution data (affybatch)
       ma1 <- MAplotPara(Dilution)

       ## MAplot to a pdf file
       pdf(file="maplot.pdf", title="AffyBatch MAplot")
       ma2 <- MAplotPara(Dilution)
       dev.off()

       stopCluster()
     }
     ## End(Not run)

