mas5                   package:xps                   R Documentation

_M_A_S _5._0 _E_x_p_r_e_s_s_i_o_n _M_e_a_s_u_r_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function converts a 'DataTreeSet' into an 'ExprTreeSet' using
     the XPS implementation of Affymetrix's MAS 5.0 expression measure.

_U_s_a_g_e:

     mas5(xps.data,
          filename   = character(0),
          filedir    = getwd(),
          tmpdir     = "",
          normalize  = FALSE,
          sc         = 500,
          option     = "transcript",
          exonlevel  = "",
          update     = FALSE,
          xps.scheme = NULL,
          add.data   = TRUE,
          verbose    = TRUE)

     xpsMAS5(object, ...)

_A_r_g_u_m_e_n_t_s:

xps.data: object of class 'DataTreeSet'.

filename: file name of ROOT data file.

 filedir: system directory where ROOT data file should be stored.

  tmpdir: optional temporary directory where temporary ROOT files
          should be stored.

normalize: logical. If 'TRUE' scale normalization is used after an
          'ExprTreeSet' is obtained.

      sc: value at which all arrays will be scaled to.

  option: option determining the grouping of probes for summarization,
          one of  'transcript', 'exon', 'probeset'; exon arrays only.

exonlevel: exon annotation level determining which probes should be
          used for summarization; exon/genome arrays only.

  update: logical. If 'TRUE' the existing ROOT data file 'filename'
          will be updated.

xps.scheme: optional alternative 'SchemeTreeSet'.

add.data: logical. If 'TRUE' expression data will be included as slot
          'data'.

 verbose: logical, if 'TRUE' print status information.

  object: object of class 'DataTreeSet'.

     ...: arguments
          'filename','filedir','tmpdir','option','exonlevel','xps.scheme'.

_D_e_t_a_i_l_s:

     This function computes the Affymetrix MAS 5.0 expression measure
     as implemented in XPS. Although this implementation is based on
     the Affymetrix 'sadd_whitepaper.pdf', it  can be used to compute
     an expression level for both expression arrays and exon arrays. 
     For exon arrays it is necessary to supply the requested 'option'
     and 'exonlevel'.

     Following 'option's are valid for exon arrays:

       'transcript':  expression levels are computed for transcript clusters, i.e. probe sets containing the same 'transcript_cluster_id'.
       'exon':        expression levels are computed for exon clusters, i.e. probe sets containing the same 'exon_id', where each exon cluster consists of one or more 'probeset's.
       'probeset':    expression levels are computed for individual probe sets, i.e. for each 'probeset_id'.

     Following 'exonlevel' annotations are valid for exon arrays:

         'core':          probesets supported by RefSeq and full-length GenBank transcripts.
         'metacore':      core meta-probesets.
         'extended':      probesets with other cDNA support.
         'metaextended':  extended meta-probesets.
         'full':          probesets supported by gene predictions only.
         'metafull':      full meta-probesets.
         'affx':          standard AFFX controls.
         'all':           combination of above (including affx).

     Following 'exonlevel' annotations are valid for whole genome
     arrays:

         'core':      probesets with category 'unique', 'similar' and 'mixed'.
         'metacore':  probesets with category 'unique' only.
         'affx':      standard AFFX controls.
         'all':       combination of above (including affx).

     Exon levels can also be combined, with following combinations
     being most useful:

       'exonlevel="metacore+affx"':       core meta-probesets plus AFFX controls
       'exonlevel="core+extended"':       probesets with cDNA support
       'exonlevel="core+extended+full"':  supported plus predicted probesets

     Exon level annotations are described in the Affymetrix whitepaper 
     'exon_probeset_trans_clust_whitepaper.pdf'.

     If 'normalize=TRUE' then the expression levels will be scaled to
     'sc'.  For 'sc=0' the expression levels will be scaled to the mean
     expression level.

     If 'update=TRUE' then the existing 'ROOT' file 'filename' will be
     updated, however, this is usually only recommended as option for
     function 'express'.

     In order to use an alternative 'SchemeTreeSet' set the
     corresponding SchemeTreeSet  'xps.scheme'.

     'xpsMAS5' is the 'DataTreeSet' method called by function 'mas5',
     however,  expression levels will not be scaled to a common mean
     expression level.

_V_a_l_u_e:

     An 'ExprTreeSet'

_N_o_t_e:

     In contrast to function 'mas5', expression levels computed with
     'xpsMAS5'  will not be scaled to a common mean expression level.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_R_e_f_e_r_e_n_c_e_s:

     Affymetrix (2002) Statistical Algorithms Description Document,
     Affymetrix Inc.,  Santa Clara, CA, whitepaper. <URL:
     http://www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf>

     Affymetrix (2005) Exon Probeset Annotations and Transcript Cluster
     Groupings, Affymetrix Inc.,  Santa Clara, CA,
     exon_probeset_trans_clust_whitepaper.pdf.

_S_e_e _A_l_s_o:

     'express'

_E_x_a_m_p_l_e_s:

     ## first, load ROOT scheme file and ROOT data file
     scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
     data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

     data.mas5 <- mas5(data.test3,"tmp_Test3MAS5",tmpdir="",normalize=TRUE,sc=500,update=TRUE,verbose=FALSE)

     ## get data.frame
     expr.mas5 <- validData(data.mas5)
     head(expr.mas5)

     ## plot results
     if (interactive()) {
     boxplot(data.mas5)
     boxplot(log2(expr.mas5))
     }

     rm(scheme.test3, data.test3)
     gc()

