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