express {xps} | R Documentation |
This function allows to combine different algorithms to compute expression levels, or to return the result for different algorithms only.
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, ...)
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. |
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.
An object of type DataTreeSet
or ExprTreeSet
.
Christian Stratowa
bgcorrect
, normalize
, summarize
## 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])) }