xps (version 1.32.0)

fitRLM: Functions for fitting RMA as probe-level model

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.

Value

An object of type QualTreeSet.

Details

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

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)