justmgMOS {puma} | R Documentation |
This function converts CEL files into an exprReslt
using mgmos.
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, gsnorm=c("median", "none", "mean", "meanlog"), savepar=FALSE, eps=1.0e-6) just.mgmos(..., 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)
... |
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 |
an AnnotatedDataFrame object. |
description |
a MIAME object. |
notes |
notes. |
background |
Logical value. If TRUE , then perform background correction before applying mgmos. |
gsnorm |
character. specifying the algorithm of global scaling normalisation. |
savepar |
Logical value. If TRUE , then the estimated parameters of the model are saved in file par_mgmos.txt and phi_mgmos.txt. |
eps |
Optimisation termination criteria. |
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.
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.
An exprReslt
.
Related class exprReslt-class
and related method mgmos