\name{ini.call}
\alias{ini.call}
\alias{xpsINICall-methods}
\alias{xpsINICall}
\title{Informative/Non-Informative Call}
\description{
Computes the Informative/Non-Informative Call for the exclusion of non-informative probe sets.
}
\usage{
ini.call(xps.data,
filename = character(0),
filedir = getwd(),
tmpdir = "",
weight = 0.5,
mu = 0.0,
scale = 1.0,
tol = 0.00001,
cyc = 100,
alpha1 = 0.4,
alpha2 = 0.6,
version = "1.3.1",
option = "transcript",
exonlevel = "",
xps.scheme = NULL,
add.data = TRUE,
verbose = TRUE)
xpsINICall(object, ...)
}
\arguments{
\item{xps.data}{object of class \code{DataTreeSet}.}
\item{filename}{file name of ROOT data file.}
\item{filedir}{system directory where ROOT data file should be stored.}
\item{tmpdir}{optional temporary directory where temporary ROOT files should be stored.}
\item{weight}{hyperparameter, usually set to 0.5 for \code{version="1.3.1"} and to 8.0
for \code{version="1.3.0"}.}
\item{mu}{hyperparameter allowing to correct for potential bias.}
\item{scale}{scaling parameter, usually set to 1.0 for \code{version="1.3.1"} and to 2.0
for \code{version="1.3.0"}.}
\item{tol}{termination tolerance for EM algorithm.}
\item{cyc}{maximum number of cycles of EM algorithm.}
\item{alpha1}{a significance threshold in (0,alpha2).}
\item{alpha2}{a significance threshold in (alpha1,1.0).}
\item{version}{version of original farms package. Currently, \code{version="1.3.1"} and
\code{version="1.3.0"} are implemented. Default is \code{version="1.3.1"}.}
\item{option}{option determining the grouping of probes for summarization, one of
\sQuote{transcript}, \sQuote{exon}, \sQuote{probeset}; exon arrays only.}
\item{exonlevel}{exon annotation level determining which probes should be used for summarization; exon/genome arrays only.}
\item{xps.scheme}{optional alternative \code{SchemeTreeSet}.}
\item{add.data}{logical. If \code{TRUE} call data will be added to slots \code{data} and \code{detcall}.}
\item{verbose}{logical, if \code{TRUE} print status information.}
\item{object}{object of class \code{DataTreeSet}.}
\item{\dots}{the arguments described above.}
}
\details{
In contrast to \code{\link{mas5.call}} this function quantifies the signal-to-noise ratio for
each probe set, as described in Talloen et al. Thus, the returned p-values and detection calls
have a different meaning:
The p-value that is returned estimates the signal-to-noise ratio (SNR): \cr
P-values (SNR) of less than 0.5 indicate that there is more signal than noise and the
corresponding genes are considered to be \sQuote{informative} for further analysis. In
contrast, values greater than 0.5 indicate \sQuote{non-informative} genes.
The informative call is computed by thresholding the p-value as in:
call \dQuote{P} if p-value < alpha1 \cr
call \dQuote{M} if alpha1 <= p-value < alpha2 \cr
call \dQuote{A} if alpha2 <= p-value
Here \dQuote{P} should be considered as informative \dQuote{I}, \dQuote{M} as marginally
informative, and \dQuote{A} as non-informative \dQuote{NI}.
The defaults for \code{alpha1=0.4} and \code{alpha2=0.6} are set to allow \dQuote{M} calls.
In order to get the same results as package \sQuote{farms\_1.3.1}, you need to set
\code{alpha1=0.5} and \code{alpha2=0.5}.
For exon/genome arrays it is necessary to supply \code{option} and \code{exonlevel}.
Following \code{option}s are valid for exon arrays only:
\tabular{ll}{
\code{transcript}: \tab expression levels are computed for transcript clusters,
i.e. probe sets containing the same \sQuote{transcript\_cluster\_id}. \cr
\code{exon}: \tab expression levels are computed for exon clusters,
i.e. probe sets containing the same \sQuote{exon\_id}, where each exon cluster
consists of one or more \code{probeset}s. \cr
\code{probeset}: \tab expression levels are computed for individual probe sets,
i.e. for each \sQuote{probeset\_id}. \cr
}
Following \code{exonlevel} annotations are valid for exon arrays:
\tabular{lll}{
\tab \code{core}:\tab probesets supported by RefSeq and full-length GenBank transcripts. \cr
\tab \code{metacore}:\tab core meta-probesets. \cr
\tab \code{extended}:\tab probesets with other cDNA support. \cr
\tab \code{metaextended}:\tab extended meta-probesets. \cr
\tab \code{full}:\tab probesets supported by gene predictions only. \cr
\tab \code{metafull}:\tab full meta-probesets. \cr
\tab \code{ambiguous}:\tab ambiguous probesets only. \cr
\tab \code{affx}:\tab standard AFFX controls. \cr
\tab \code{all}:\tab combination of above.
}
Following \code{exonlevel} annotations are valid for whole genome arrays:
\tabular{lll}{
\tab \code{core}:\tab probesets with category \sQuote{unique} and \sQuote{mixed}. \cr
\tab \code{metacore}:\tab probesets with category \sQuote{unique} only. \cr
\tab \code{affx}:\tab standard AFFX controls. \cr
\tab \code{all}:\tab combination of above.
}
Exon levels can also be combined, with following combinations being most useful:
\tabular{ll}{
\code{exonlevel="metacore+affy"}: \tab core meta-probesets plus AFFX controls \cr
\code{exonlevel="core+extended"}: \tab probesets with cDNA support \cr
\code{exonlevel="core+extended+full"}: \tab supported plus predicted probesets \cr
}
Exon level annotations are described in the Affymetrix whitepaper
\sQuote{exon\_probeset\_trans\_clust\_whitepaper.pdf}.
In order to use an alternative \code{\link{SchemeTreeSet}} set the corresponding
SchemeTreeSet \code{xps.scheme}.
\code{xpsINICall} is the \code{DataTreeSet} method called by function \code{ini.call},
containing the same parameters.
}
\value{
A \code{\link{CallTreeSet}}
}
\author{Christian Stratowa}
\note{
Since I/NI-calls distinguish only between informative and non-informative genes, the
calls are identical for all samples.
}
\references{
Talloen, W., Clevert D.-A., Hochreiter, S., Amaratunga, D., Bijnens, J., Kass, S., and
Gohlmann, H.W.H. (2006), I/NI-calls for the exclusion of non-informative genes: a highly
effective filtering tool for microarray data. Bioinformatics 23(21):2897-2902
}
\seealso{\code{\link{farms}}, \code{\link{mas5.call}}}
\examples{
## 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="/"))
## I/NI call
call.ini <- ini.call(data.test3,"tmp_Test3INI",verbose=FALSE)
## get data.frames
snr.ini <- pvalData(call.ini)
inf.ini <- presCall(call.ini)
head(snr.ini)
head(inf.ini)
## plot results
if (interactive()) {
callplot(call.ini)
}
rm(scheme.test3, data.test3)
gc()
}
\keyword{manip}