| normalize {xps} | R Documentation |
Functions that allow to normalize Affymetrix arrays both at the probe level (“low-level normalization”) and/or at the expression level (“high-level normalization”).
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), 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), 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), verbose = TRUE) normalize.quantiles(xps.data, filename = character(0), filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = "", 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), verbose = TRUE) xpsNormalize(object, ...)
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. |
verbose |
logical, if TRUE print status information. |
object |
object of class DataTreeSet or ExprTreeSet. |
... |
the arguments described above. |
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.
An object of type DataTreeSet or ExprTreeSet.
Functions normalize.lowess and normalize.supsmu have only be tested
for objects of type ExprTreeSet but not for objects of type
DataTreeSet, i.e. for probe level intensities.
Christian Stratowa
## 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)