normalize                package:xps                R Documentation

_N_o_r_m_a_l_i_z_a_t_i_o_n _o_n _A_f_f_y_m_e_t_r_i_x _P_r_o_b_e _L_e_v_e_l _D_a_t_a _o_r _o_n _E_x_p_r_e_s_s_i_o_n _L_e_v_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Functions that allow to normalize Affymetrix arrays both at the
     probe level ("low-level normalization") and/or at the expression
     level ("high-level normalization").

_U_s_a_g_e:

     normalize(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, select = "all", method = "mean", option = "transcript:all", logbase = "0", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.02, 0), add.data = TRUE, verbose = TRUE)

     normalize.constant(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, method = "mean", logbase = "0", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.02, 0), add.data = TRUE, verbose = TRUE)

     normalize.lowess(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, logbase = "log2", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.67, 3), add.data = TRUE, verbose = TRUE)

     normalize.quantiles(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", add.data = TRUE, verbose = TRUE)

     normalize.supsmu(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, logbase = "log2", exonlevel = "", refindex = 0, refmethod = "mean", params = list(0.67, 3), add.data = TRUE, verbose = TRUE)

     xpsNormalize(object, ...)

_A_r_g_u_m_e_n_t_s:

xps.data: object of class 'DataTreeSet' or 'ExprTreeSet'.

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 normalization.

  method: normalization method to use.

  option: option determining the grouping of probes for normalization,
          and the selection of the probes.

 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.

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

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

  params: vector of parameters for normalization method.

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' or 'ExprTreeSet'.

     ...: the arguments described above.

_D_e_t_a_i_l_s:

     Functions that allow to normalize Affymetrix arrays both at the
     probe level ("low-level normalization") and/or at the expression
     level ("high-level normalization").

     'xpsNormalize' are the 'DataTreeSet' or 'ExprTreeSet' methods,
     respectively, called by function 'normalize', containing the same
     parameters.

_V_a_l_u_e:

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

_W_a_r_n_i_n_g:

     Functions 'normalize.lowess' and 'normalize.supsmu' have only be
     tested for 'object's of type 'ExprTreeSet' but not for objects of
     type  'DataTreeSet', i.e. for probe level intensities.

_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_Test3NormRMA",filedir=getwd(),tmpdir="",verbose=FALSE)
     ## normalize quantiles
     data.qu.rma <- normalize.quantiles(data.bg.rma,"tmp_Test3NormRMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)
     ## summarize medianpolish
     data.mp.rma <- summarize.rma(data.qu.rma,"tmp_Test3NormRMA",filedir=getwd(),tmpdir="",update=TRUE,verbose=FALSE)

