express                 package:xps                 R Documentation

_C_o_m_p_u_t_e _e_x_p_r_e_s_s_i_o_n _l_e_v_e_l_s _f_r_o_m _r_a_w _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This function allows to combine different algorithms to compute
     expression levels, or to return the result for different
     algorithms only.

_U_s_a_g_e:

     express(xps.data,
             filename = character(),
             filedir = getwd(),
             tmpdir = "",
             update = FALSE,
           # background correction
             bgcorrect.method = NULL,
             bgcorrect.select = character(),
             bgcorrect.option = character(),
             bgcorrect.params = list(),
           # normalization
             normalize.method = NULL,
             normalize.select = character(),
             normalize.option = character(),
             normalize.logbase = character(),
             normalize.params = list(),
           # expression values
             summarize.method = NULL,
             summarize.select = character(),
             summarize.option = character(),
             summarize.logbase = character(),
             summarize.params = list(),
           # reference values
             reference.index  = 0,
             reference.method = "mean",
             reference.params = list(0),
           # misc.
             exonlevel  = "",
             xps.scheme = NULL,
             add.data   = TRUE,
             verbose    = TRUE)

     xpsPreprocess(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.

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

bgcorrect.method: background method to use.

bgcorrect.select: type of probes to select for background correction.

bgcorrect.option: type of background correction to use.

bgcorrect.params: vector of parameters for background method.

normalize.method: normalization method to use.

normalize.select: type of probes to select for normalization.

normalize.option: normalization option.

normalize.logbase: logarithm base as character, one of '0', 'log',
          'log2', 'log10'.

normalize.params: vector of parameters for normalization method.

summarize.method: summarization method to use.

summarize.select: type of probes to select for summarization.

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

summarize.logbase: logarithm base as character, one of '0', 'log',
          'log2', 'log10'.

summarize.params: vector of parameters for summarization method.

reference.index: index of reference tree to use, or 0.

reference.method: for 'refindex=0', either trimmed mean or median of
          trees.

reference.params: vector of parameters for reference method.

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

xps.scheme: optional alternative 'SchemeSet'.

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

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

  object: object of class 'DataSet'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     This function allows to combine different algorithms to compute
     expression levels, or to return the result for different
     algorithms only.

     'xpsPreprocess' is the 'DataSet' method called by function
     'express', containing the same parameters.

_V_a_l_u_e:

     An object of type 'DataTreeSet' or 'ExprTreeSet'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'bgcorrect', 'normalize', 'summarize'

_E_x_a_m_p_l_e_s:

     ## load existing 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="/"))

     ## compute rma with a single call to express()
     expr.rma <- express(data.test3,"tmp_Test3Exprs",filedir=getwd(),tmpdir="",update=FALSE,
                 bgcorrect.method="rma",bgcorrect.select="none",bgcorrect.option="pmonly:epanechnikov",bgcorrect.params=c(16384),
                 normalize.method="quantile",normalize.select="pmonly",normalize.option="transcript:together:none",normalize.logbase="0",normalize.params=c(0.0),
                 summarize.method="medianpolish",summarize.select="pmonly",summarize.option="transcript",summarize.logbase="log2",summarize.params=c(10, 0.01, 1.0),
                 verbose=FALSE)

     ## get expression data.frame
     expr <- exprs(expr.rma)
     head(expr)

     ## plot expression levels
     if (interactive()) {
     boxplot(expr.rma)
     boxplot(log2(expr[,3:6]))
     }

