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puma (version 3.12.0)

justmmgMOS: Compute mmgmos Directly from CEL Files

Description

This function converts CEL files into an exprReslt using mmgmos.

Usage

justmmgMOS(..., filenames=character(0), widget=getOption("BioC")$affy$use.widgets, compress=getOption("BioC")$affy$compress.cel, celfile.path=getwd(), sampleNames=NULL, phenoData=NULL, description=NULL, notes="", background=TRUE, gsnorm=c("median", "none", "mean", "meanlog"), savepar=FALSE, eps=1.0e-6)


just.mmgmos(..., filenames=character(0), phenoData=new("AnnotatedDataFrame"), description=NULL, notes="", compress=getOption("BioC")$affy$compress.cel, background=TRUE, gsnorm=c("median", "none", "mean", "meanlog"), savepar=FALSE, eps=1.0e-6)

Arguments

...
file names separated by comma.
filenames
file names in a character vector.
widget
a logical specifying if widgets should be used.
compress
are the CEL files compressed?
celfile.path
a character denoting the path where cel files locate.
sampleNames
a character vector of sample names to be used in the FeatureSet.
phenoData
an AnnotatedDataFrame object.
description
a MIAME object
notes
notes
background
Logical value. If TRUE, then perform background correction before applying mmgmos.
gsnorm
character. specifying the algorithm of global scaling normalisation.
savepar
Logical value. If TRUE, the the estimated parameters of the model are saved in file par\_mmgmos.txt and phi\_mmgmos.txt.
eps
Optimisation termination criteria.

Value

An exprReslt.

Details

This method should require much less RAM than the conventional method of first creating an FeatureSet and then running mmgmos. Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

The algorithms of global scaling normalisation can be one of "median", "none", "mean", "meanlog". "mean" and "meanlog" are mean-centered normalisation on raw scale and log scale respectively, and "median" is median-centered normalisation. "none" will result in no global scaling normalisation being applied.

See Also

Related class exprReslt-class and related method mmgmos