justmgMOS {mmgmos}R Documentation

Compute mgmos Directly from CEL Files

Description

This function converts CEL files into an exprReslt using mgmos.

Usage

justmgMOS(..., 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, savepar=FALSE, eps=1.0e-6)

just.mgmos(..., filenames=character(0),
          phenoData=new("phenoData"),
          description=NULL,
          notes="",
          compress=getOption("BioC")$affy$compress.cel,
          background=TRUE, 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 ReadAffy should look for cel files
sampleNames a character vector of sample names to be used in the AffyBatch
phenoData a phenoData object
description a MIAME object
notes notes
background Logical value. If TRUE, perform background correction before applying mgmos.
savepar Logical value. If TRUE the estimated parameters of the model are saved in file par_mgmos.txt and phi_mgmos.txt.
eps Optimisation termination criteria.

Details

This method should require much less RAM than the conventional method of first creating an AffyBatch and then running mgmos.

Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.

Value

An exprReslt.

See Also

Related class exprReslt-class and related method mgmos

Examples



[Package mmgmos version 1.4.0 Index]