| normAffy {EMA} | R Documentation |
This function converts .cel files into a matrix of normalised data using GCRMA, RMA or MAS5 normalisation.
normAffy(filenames, celfile.path, method = c("GCRMA","RMA","MAS5"),
cdfname = NULL, rmaffx = TRUE, fast=TRUE)
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 |
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.
A matrix containing the normalised data, genes on rows and samples on columns.
## Not run: ## GCRMA normalisation normData <- normAffy(celfile.path="PathToCelFiles", method="GCRMA") ## End(Not run)