mas4                   package:xps                   R Documentation

_M_A_S _4._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 4.0 expression measure.

_U_s_a_g_e:

     mas4(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)

     xpsMAS4(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 4.0 expression measure,
     i.e. the  'Average Difference' expression level, as implemented in
     XPS.

     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.

     'xpsMAS4' is the 'DataTreeSet' method called by function 'mas4',
     however,  expression levels will not be scaled to a common mean
     expression level.

     For further details see 'mas5'.

_V_a_l_u_e:

     An 'ExprTreeSet'

_N_o_t_e:

     In contrast to function 'mas4', expression levels computed with
     'xpsMAS4'  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 (1999) GeneChip Expression Analysis Algorithm Tutorial,
     Affymetrix Inc.,  Santa Clara, CA.

_S_e_e _A_l_s_o:

     'xpsMAS4', '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.mas4 <- mas4(data.test3,"tmp_Test3MAS4",tmpdir="",normalize=TRUE,sc=500, update=TRUE,verbose=FALSE)

     ## get data.frame
     expr.mas4 <- validData(data.mas4)
     head(expr.mas4)

     ## plot results (negative expression values!)
     if (interactive()) {
     boxplot(expr.mas4)
     }

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

