fitRLM: Functions for fitting RMA as probe-level model

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Convert Affymetrix probe level data to expression levels by fitting RMA as multichip model.

Usage

fitRLM(xps.data,
       filename   = character(),
       filedir    = getwd(),
       tmpdir     = "",
       background = "pmonly",
       normalize  = TRUE,
       qualopt    = "all",
       option     = "transcript",
       exonlevel  = "",
       params     = list(16384, 0.0, 1.0, 10, 0.01, 1),
       xps.scheme = NULL,
       add.data   = FALSE,
       bufsize    = 32000,
       verbose    = TRUE)

rmaPLM(xps.data,
       filename   = character(),
       filedir    = getwd(),
       tmpdir     = "",
       background = "pmonly",
       normalize  = TRUE,
       qualopt    = "all",
       option     = "transcript",
       exonlevel  = "",
       params     = list(16384, 0.0, 1.0, 10, 0.01, 1),
       xps.scheme = NULL,
       add.data   = FALSE,
       bufsize    = 32000,
       verbose    = TRUE)

Arguments

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.
background	probes used to compute background, one of ‘pmonly’, ‘mmonly’, ‘both’; for genome/exon arrays one of ‘genomic’, ‘antigenomic’
normalize	logical. If TRUE normalize data using quantile normalization.
qualopt	option determining the data to which to apply qualification, one of ‘raw’, ‘adjusted’, ‘normalized’, ‘all’.
option	option determining the grouping of probes for qualification, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
exonlevel	exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
params	list of (default) parameters for rma.
xps.scheme	optional alternative SchemeSet.
add.data	logical. If TRUE expression data will be included as slot data.
bufsize	integer which sets the buffer size of the tree branch baskets (default is 32000).
verbose	logical, if TRUE print status information.

Details

Convert Affymetrix probe level data to expression levels by fitting RMA as multichip model.

Value

An object of type QualTreeSet.

Author(s)

Christian Stratowa

See Also

fitQC, qualify, express

Examples

## Not run: 
## 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="/"))

## qualification - rlm
rlm.all <- rmaPLM(data.test3, "tmp_Test3RLMall", filedir=getwd(), tmpdir="", qualopt="all", option="transcript", add.data=FALSE)

## get borders
brd.rlm.all <- borders(rlm.all)

## get residuals
res.rlm.all <- residuals(rlm.all)

## get weights
w.rlm.all <- weights(rlm.all)

## plot expression levels
if (interactive()) {
coiplot(rlm.all)
borderplot(rlm.all)
nuseplot(rlm.all)
rleplot(rlm.all)
image(rlm.all, type="resids")
}

## End(Not run)

xps documentation built on Nov. 8, 2020, 6 p.m.