rmaPreprocessing: RMA pre-process '.CEL' files

In oncoclass/hemaClass: One-by-one normalization and classification of hematological malignacies

Description

Pre-process .CEL files read into R using readCelfiles according to the regular cohort RMA method and create a reference for later use.

Usage

rmaPreprocessing(affy.batch, test = FALSE, quantile = NULL)

Arguments

affy.batch	An object created by readCelfiles.
test	Should the .CEL files be tested. When set to TRUE bad .CEL files are automatically discarded.
quantile	Specify a vector of quantiles that the data should be normalized to.

Value

Returns a list of length 9 with the slots:

exprs	The cohort RMA pre-processed log_2-expression matrix
exprs.sc	As slot $exprs but scaled to have zero median and unit variance.
exprs.sc.mean	As slot $exprs but scaled to have zero mean and unit variance.
quantile	The values defining the distribution used in quantile normalization.
alpha	The alpha values of the RMA summarization.
sd	A numeric of the standard errors of each feature.
median	A numeric with the medians for each feature.
mean	A numeric with the means for each feature.
bad	A character giving the 'bad' arrays. NULL if no bad arrays are found or when test = FALSE

Author(s)

Steffen Falgreen <sfl (at) rn.dk>
Anders Ellern Bilgrau <abilgrau (at) math.aau.dk>

References

http://hemaClass.org

See Also

rmaReference for one-by-one reference based RMA normalization.

Examples

# List .CEL files bundled with hemaClass
files <- list.files(system.file("extdata/celfiles", package = "hemaClass"),
                    full.names = TRUE)
affy.batch <- readCelfiles(filenames = files[1:3]) # Read three first files

# RMA normalize
affy.rma <- rmaPreprocessing(affy.batch)
str(affy.rma)

oncoclass/hemaClass documentation built on May 24, 2019, 2:19 p.m.