dfw                   package:xps                   R Documentation

_D_i_s_t_r_i_b_u_t_i_o_n _F_r_e_e _W_e_i_g_h_t_e_d _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 Distribution Free Weighted Fold Change (DFW) method.

_U_s_a_g_e:

     dfw(xps.data,
         filename   = character(0),
         filedir    = getwd(),
         tmpdir     = "",
         normalize  = TRUE,
         m          = 3,
         n          = 1,
         c          = 0.01,
         option     = "transcript",
         exonlevel  = "",
         xps.scheme = NULL,
         add.data   = TRUE,
         verbose    = TRUE)

_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' normalize data using quantile
          normalization.

       m: positive number as exponent of the weighted range WR.

       n: positive number as exponent of the weighted standard
          deviation WSD.

       c: scaling parameter.

  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.

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.

_D_e_t_a_i_l_s:

     This function computes the DFW (Distribution Free Weighted Fold
     Change) expression measure  described in Chen et al. 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+affy"':       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: 
       "Exon Probeset Annotations and Transcript Cluster Groupings".

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

_V_a_l_u_e:

     An 'ExprTreeSet'

_N_o_t_e:

     The expression measure obtained with DFW is given in linear scale,
     analogously to the expression  measures computed with 'mas5' and
     'rma'. 

     For the analysis of many exon arrays it may be better to define a
     'tmpdir', since this will store only the results in the main file
     and not e.g. background and normalized intensities, and thus will
     reduce the file size of the main file. For quantile normalization
     memory should not be an issue, however DFW depends on RAM unless
     you are using a temporary file.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_R_e_f_e_r_e_n_c_e_s:

     Chen, Z., McGee M., Liu Q., and Scheuermann, R.H. (2007), A
     distribution free summarization  method for Affymetrix GeneChip
     arrays. Bioinformatics 23(3):321-327

_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.dfw <- dfw(data.test3,"tmp_Test3DFW",verbose=FALSE)

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

