rmaReference: RMA pre-process '.CEL' files read

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

Description

Pre-process .CEL files according to the one-by-one RMA method using a reference build using rmaPreprocessing.

Usage

rmaReference(affy.batch, reference, test = FALSE)

Arguments

affy.batch	An affy.batch object, usually created by readCelfiles.
reference	An RMA reference object created by rmaPreprocessing.
test	Should the supplied .CEL files be qualtiy tested. When set to TRUE bad .CEL files are automatically discarded.

Value

Returns a list of length 3 with the slots:

exprs	The one-by-one 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.

Author(s)

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

References

http://hemaClass.org

See Also

rmaPreprocessing, readCelfiles

Examples

# List .CEL files bundled with hemaClass
files <- list.files(system.file("extdata/celfiles", package = "hemaClass"),
                    full.names = TRUE)
affy.batch <- readCelfiles(files) # Read in the .CEL files

# Build references
ref.affy   <- rmaPreprocessing(affy.batch)
ref.affy.2 <- rmaPreprocessing(affy.batch, quantile = ref.affy$quantile)
all(ref.affy.2$exprs - ref.affy$exprs < 0.00000001)

# Or use build-in:
ref.affy <- readCHEPRETROreference()

# RMA one-by-one pre-process using the reference:
user.affy  <- rmaReference(affy.batch, ref.affy)

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