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), 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, ...)
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. |
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 object
s 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)