EMA (version 1.4.7)

normAffy: Normalisation of Affymetrix expression arrays

Description

This function converts .cel files into a matrix of normalised data using GCRMA, RMA or MAS5 normalisation.

Usage

normAffy(filenames, celfile.path, method = c("GCRMA","RMA","MAS5"),
cdfname = NULL, rmaffx = TRUE, fast=TRUE)

Arguments

filenames

The .CEL files to normalize separated by comma, if empty the celfile.path.

celfile.path

Path to the directory containing the cel files

method

Normalisation method to use

cdfname

Used to specify the name of an alternative cdf package. If set to NULL, the usual cdf package based on Affymetrix' mappings will be used. Note that the name should not include the 'cdf' on the end, and that the corresponding probe package is also required to be installed. If either package is missing an error will result.

rmaffx

boolean, indicating wether the probe control should be removed

fast

logical, option of GCRMA normalisation. see details

Value

A matrix containing the normalised data, genes on rows and samples on columns.

Details

This function allows to use several normalisation methods. It is a wrapper for functions justRMA,justGCRMA and mas5 from packages affy and gcrma.\ The fast parameter of the justRMA can lead to different results. If fast is true, the Lim et al. correction is applied. All expression values smaller than a threshold are put to the same values, leading to a sharp pick on the left of the distribution. Set fast to false to obtain a standard GCRMA distribution.

If the filenames parameter is missing, then all the files of the celfile.path are used.

Examples

# NOT RUN {
## GCRMA normalisation
normData <- normAffy(celfile.path="PathToCelFiles", method="GCRMA")
# }
# NOT RUN {
# }