exprMat: Calculate the expression matrix from the raw expression data.

In gibbslab/coexnet: coexnet: An R package to build CO-EXpression NETworks from Microarray Data

Description

This function use a affyBatch object with the raw expression data to normalize and transform the matrix from probeset to gene considering the option to remove the batch effect in the long microarray data.

Usage

exprMat(affy, genes, NormalizeMethod, SummaryMethod, BatchCorrect = TRUE)

Arguments

affy	A AffyBatch object with the raw expression data.
genes	A table with two columns, in the firt one the name of each probe in the microarray with header "probe" and in the second one the corresponding gene or ID with header "ID".
NormalizeMethod	The method to normalize the raw data. Can be "vsn" to apply Variance Stabilizing Normalization function or "rma" to apply Robust Multi-Array Average function.
SummaryMethod	The method to pass from probeset to genes or ID. Can be "max" to selecto the probeset with the most average expression value or "median" to obtain the median of each sample of the set of probeset corresponding to particular gen or ID.
BatchCorrect	The option to apply batch effect correction, by default TRUE.

Value

A SummarizedExperiment object with the expression matrix.

Author(s)

Juan David Henao <[e-mail]>

References

Huber, W., Von Heydebreck, A., Sultmann, H., Poustka, A., & Vingron, M. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18(suppl 1), S96-S104.

Irizarry, R. A., Hobbs, B., Collin, F., Beazer Barclay, Y. D., Antonellis, K. J., Scherf, U., & Speed, T. P. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2), 249-264.

See Also

getAffy to obtain the affyBatch object.

geneSymbol to obtain the data.frame with probeset and genes/ID from .SOFT file.

Examples

## Not run: 

# Loading data

if (require(affydata)) {
 data(Dilution)
}

# Loading table with probeset and gene/ID information

data(info)

# Calculating the expression matrix

## RMA

rma <- exprMat(affy = Dilution,genes = info,NormalizeMethod = "rma",
SummaryMethod = "median",BatchCorrect = FALSE)
head(rma)

## VSN

vsn <- exprMat(affy = Dilution,genes = info,NormalizeMethod = "vsn",
SummaryMethod = "median",BatchCorrect = FALSE)
head(vsn)


## End(Not run)

gibbslab/coexnet documentation built on May 17, 2019, 4:19 a.m.