justRMA {affy} | R Documentation |
Read CEL files and compute an expression measure without using an AffyBatch.
just.rma(..., filenames = character(0), phenoData = new("AnnotatedDataFrame"), description = NULL, notes = "", compress = getOption("BioC")$affy$compress.cel, rm.mask = FALSE, rm.outliers = FALSE, rm.extra = FALSE, verbose=FALSE, background=TRUE, normalize=TRUE, bgversion=2, destructive=FALSE, cdfname = NULL) justRMA(..., 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="", rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, hdf5=FALSE, hdf5FilePath=NULL,verbose=FALSE, normalize=TRUE, background=TRUE, bgversion=2, destructive=FALSE, cdfname = NULL)
... |
file names separated by comma. |
filenames |
file names in a character vector. |
phenoData |
a AnnotatedDataFrame object |
description |
a MIAME object |
notes |
notes |
compress |
are the CEL files compressed ? |
rm.mask |
should the spots marked as 'MASKS' set to NA ? |
rm.outliers |
should the spots marked as 'OUTLIERS' set to NA |
rm.extra |
if TRUE , overrides what is in rm.mask and rm.oultiers |
hdf5 |
use of hdf5 ? (not available yet) |
hdf5FilePath |
a filename to use with hdf5 (not available yet) |
verbose |
verbosity flag |
widget |
a logical specifying if widgets should be used. |
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 |
normalize |
logical value. If TRUE normalize data using
quantile normalization |
background |
logical value. If TRUE background correct
using RMA background correction |
bgversion |
integer value indicating which RMA background to use 1: use background similar to pure R rma background given in affy version 1.0 - 1.0.2 2: use background similar to pure R rma background given in affy version 1.1 and above |
destructive |
logical value. If TRUE works on the PM matrix in place as much as possible, good for large datasets. |
cdfname |
Used to specify the name of an alternative cdf package. If set to
NULL , the usual cdf package based on Affymetrix' mappings
will be used. |
justRMA
is a wrapper for just.rma
that permits the
user to read in phenoData, MIAME information, and CEL files using
widgets. One can also define files where to read phenoData and MIAME
information.
If the function is called with no arguments justRMA()
then all the CEL
files in the working directory are read, converted to an expression
measure using RMA and put into an ExpressionSet
.
However, the arguments give the user great flexibility.
phenoData
is read using read.AnnotatedDataFrame
. If a
character is given it tries to read the file with that name
to obtain the phenoData
object as described in read.AnnotatedDataFrame
. If left
NULL
and widget=FALSE
(widget=TRUE
is not currently
supported) then a default object is created.
It will be an object of class AnnotatedDataFrame
with
pData a data.frame with column x indexing the CEL files.
description
is read using read.MIAME
. If a
character is given it tries to read the file with that name to obtain a
MIAME
instance. If left
NULL
but widget=TRUE
then widgets are used. If left
NULL
and widget=FALSE
then an empty instance of
MIAME
is created..
The arguments rm.masks
, rm.outliers
, rm.extra
are
passed along to the function read.celfile
.
An ExpressionSet
object, containing expression values identical to
what one would get from running rma
on an AffyBatch
.
In the beginning: James MacDonald <jmacdon@med.umich.edu> Supporting routines, maintenance and just.rma: Ben Bolstad <bmb@bmbolstad.com>