summarize                package:xps                R Documentation

_P_r_o_b_e _S_e_t _S_u_m_m_a_r_i_z_i_n_g _F_u_n_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Converts Affymetrix probe level data to expression levels by
     summarizing the probe set values into one expression measure and a
     standard error for this summary.

_U_s_a_g_e:

     summarize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "none", method = character(), option = "transcript", logbase = "0", exonlevel = "", params = list(), xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

     summarize.mas4(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, option = "transcript", exonlevel = "", xps.scheme = NULL, add.data = TRUE, verbose = TRUE)

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

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

     xpsSummarize(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.

  select: type of probes to select for summarization.

  method: summarization method to use.

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

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

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

  params: vector of parameters for summarization method.

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'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     Converts Affymetrix probe level data to expression levels by
     summarizing the probe set values into one expression measure and a
     standard error for this summary.

     'xpsSummarize' is the 'DataTreeSet' method called by function
     'summarize', containing the same parameters.

_V_a_l_u_e:

     An 'ExprTreeSet'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_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="/"))

     ## RMA background
     data.bg.rma <- bgcorrect.rma(data.test3,"tmp_Test3RMA",filedir=getwd(),tmpdir="",verbose=FALSE)
     ## normalize quantiles
     data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)
     ## summarize medianpolish
     data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3RMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)

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

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

