| justGCRMA {gcrma} | R Documentation |
This function converts CEL files into an exprSet
using the robust multi-array average (RMA) expression measure with help of probe sequences.
just.gcrma <- function(..., filenames=character(0),
phenoData=new("phenoData"),
description=NULL,
notes="", compress=getOption("BioC")$affy$compress.cel,
normalize=TRUE, bgversion=2, affinity.info=NULL,
type=c("fullmodel","affinities","mm","constant"),
k=6*fast+0.5*(1-fast), stretch=1.15*fast+1*(1-fast),
correction=1, rho=0.7, optical.correct=TRUE,
verbose=TRUE, fast=TRUE, minimum=1, optimize.by=c("speed","memory"))
justGCRMA <- function(..., 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="",
normalize=TRUE,
bgversion=2, affinity.info=NULL,
type=c("fullmodel","affinities","mm","constant"),
k=6*fast+0.5*(1-fast), stretch=1.15*fast+1*(1-fast),
correction=1, rho=0.7, optical.correct=TRUE,
verbose=TRUE, fast=TRUE, minimum=1, optimize.by=c("speed","memory"))
... |
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 ? |
phenoData |
a phenoData object |
description |
a MIAME object |
notes |
notes |
affinity.info |
NULL or a list of three components:
apm,amm and index, for PM probe
affinities, MM probe affinities, the index of probes with known
sequence, respectively. |
type |
"fullmodel" for sequence and MM model. "affinities" for sequence information only. "mm" for using MM without sequence information. |
k |
A tuning factor. |
rho |
correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7 |
stretch |
|
correction |
. |
normalize |
logical value. If TRUE normalize data using
quantile normalization |
optical.correct |
Logical value. If TRUE, optical
background correction is performed. |
verbose |
Logical value. If TRUE messages about the progress of
the function is printed. |
fast |
Logicalvalue. If TRUE a faster add-hoc algorithm is
used. |
optimize.by |
"speed" will use a faster algorithm but more RAM, and "memory" will be slower, but require less RAM. |
This method should require much less RAM than the conventional
method of first creating an AffyBatch and then running
gcrma.
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 tuning factor k will have different meanings if one uses
the fast (add-hoc) algorithm or the empirical bayes approach. See Wu
et al. (2003)
fast.bkg and mem.bkg are two internal functions.
An exprSet.
James W. MacDonald