summarize: LVSmiRNA Summarization Function(s) for microRNA Microarray

In LVSmiRNA: LVS normalization for Agilent miRNA data

Description

Summarize microRNA microarray data objects.

Usage

summarize(object, ...)
## S3 method for class 'EList'
summarize(object,RA,remove.ctrl=FALSE,is.log=!is.null(object$preprocessing$Normalization),
method=c("rlm","medianpolish","mean"),verbose=FALSE,make.exprs=FALSE,...)
## S3 method for class 'RGList'
summarize(object,RA,remove.ctrl=FALSE,is.log=!is.null(object$preprocessing$Normalization),
method=c("rlm","medianpolish","mean"),verbose=FALSE,make.exprs=FALSE,...)

Arguments

object	an object for which a summary is desired.
RA	an object from estVC.
remove.ctrl	logical, indicating whether to remove control probes.
is.log	Are data already logged?
method	currently, method "medianpolish","mean" and "rlm" are supported.
verbose	More output
make.exprs	Should the output be and exprSet object?
...	...

Details

For multi-probe, multi-replicate microarray, intensities need to be summarized into a single expression value for each miRNA. The data objects are summarized as if they were lists.

Value

An Elist object containing components as follows:

G	matrix containing the summarized intensities for each array with miRNAs as rows and arrays as columns.
Gb	matrix containing the background intensities for each array with probes as rows and arrays as columns.
targets	data frame with column FileName giving the names of the files read, with column Sample giving the names of the samplse.
genes	data frame containing annotation information about the probes, for examples gene names and IDs and positions on the array.
source	character string giving the image analysis program name.
preprocessing	list with components Background, Normalization, is.log, Summarization indicate which pre-processing step has been done.

Author(s)

Stefano Calza <[e-mail]>, Suo Chen and Yudi Pawitan.

References

Irizarry et al., 'Exploration, normalization, and summaries of high density oligonucleotide array probe level data', (2003a, Biostatistics); Huber, P. J., 'Robust estimation of a location parameter', (1964, Annuas of Mathematical Statistics)

See Also

lvs, estVC

Examples

## Not run: 

data("MIR-spike-in")
AA <- estVC(MIR,method="joint")
dd <- summarize(MIR,RA=AA,method="rlm")

##summarization methods other than rlm, object RA is not required
dd1 <- summarize(MIR,method="medianpolish")
dd2 <- summarize(MIR,method="mean")

## End(Not run)

LVSmiRNA documentation built on Oct. 31, 2019, 5:29 a.m.