第1页 / 共67页
第2页 / 共67页
第3页 / 共67页
第4页 / 共67页
第5页 / 共67页
第6页 / 共67页
第7页 / 共67页
第8页 / 共67页
affy使用指南.pdf
.setAffyOptions
affy-deprecated
affy-options
affy.scalevalue.exprSet
AffyBatch-class
AffyRNAdeg
barplot.ProbeSet
bg.adjust
bg.correct
cdfenv.example
cdfFromBioC
cleancdfname
debug.affy123
expresso
expressoWidget
fit.li.wong
generateExprSet-method
generateExprVal
generateExprVal.method.avgdiff
generateExprVal.method.playerout
hlog
justRMA
list.celfiles
MAplot
mas5
mas5calls
merge.AffyBatch
mva.pairs
normalize-methods
normalize.constant
normalize.contrasts
normalize.invariantset
normalize.loess
normalize.qspline
normalize.quantiles
normalize.quantiles.robust
pairs.AffyBatch
plot.ProbeSet
plotDensity
plotLocation
pmcorrect
ppsetApply
probeMatch-methods
probeNames-methods
ProbeSet-class
ProgressBarText-class
read.affybatch
read.probematrix
rma
SpikeIn
summary
tukey.biweight
whatcdf
xy2indices
Index
Package ‘affy’
June 14, 2014
Version 1.42.2
Title Methods for Affymetrix Oligonucleotide Arrays
Author Rafael A. Irizarry , Laurent Gautier
, Benjamin Milo Bolstad , and Crispin Miller
with contributions from Magnus
Astrand , Leslie M. Cope
, Robert Gentleman, Jeff Gentry, Conrad
Halling , Wolfgang Huber, James
MacDonald , Benjamin I. P. Rubinstein,Christopher Work-
man , John Zhang
Maintainer Rafael A. Irizarry
Depends R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
Imports affyio (>= 1.13.3), BiocInstaller, graphics, grDevices,methods, preprocess-
Core, stats, utils, zlibbioc
Suggests tkWidgets (>= 1.19.0), affydata, widgetTools
LinkingTo preprocessCore
Description The package contains functions for exploratory
oligonucleotide array analysis. The dependence on tkWidgets
only concerns few convenience functions. 'affy' is fully functional without it.
License LGPL (>= 2.0)
Collate ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R
getCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R
bg.Affy.chipwide.R bg.R expresso.R fit.li.wong.R generateExprVal.method.avgdiff.R
generateExprVal.method.liwong.R generateExprVal.method.mas.R
generateExprVal.method.medianpolish.R generateExprVal.method.playerout.R hlog.R justrma.R
loess.normalize.R maffy.R mas5.R merge.AffyBatch.R
normalize.constant.R normalize.contrasts.R
normalize.invariantset.R normalize.loess.R normalize.qspline.R
normalize.quantiles.R pairs.AffyBatch.R plot.density.R
1
2
R topics documented:
plotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R
mva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R
tukey.biweight.R whatcdf.R xy2indices.R zzz.R
biocViews Microarray, OneChannel, Preprocessing
LazyLoad yes
R topics documented:
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
3
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
.
.setAffyOptions .
4
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
.
affy-deprecated .
4
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
affy-options .
.
.
5
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
affy.scalevalue.exprSet
6
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
.
AffyBatch-class .
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9
.
.
AffyRNAdeg .
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
.
.
barplot.ProbeSet .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
.
.
.
bg.adjust .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
.
bg.correct
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
.
.
cdfenv.example .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
.
.
.
cdfFromBioC .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
.
.
.
cleancdfname .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
.
.
.
debug.affy123 .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
.
expresso .
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
.
.
.
expressoWidget
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
fit.li.wong .
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
generateExprSet-method .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
generateExprVal .
.
generateExprVal.method.avgdiff
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
generateExprVal.method.playerout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
hlog .
.
.
.
.
.
justRMA .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
list.celfiles .
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
.
MAplot
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
mas5 .
.
.
.
.
.
mas5calls .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
.
merge.AffyBatch .
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
mva.pairs
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
normalize-methods .
.
.
normalize.constant
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
normalize.contrasts .
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
normalize.invariantset .
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
.
.
normalize.loess .
.
.
.
normalize.qspline .
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
normalize.quantiles .
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
normalize.quantiles.robust
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
.
pairs.AffyBatch .
plot.ProbeSet
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.setAffyOptions
3
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
plotDensity .
.
plotLocation .
.
pmcorrect
.
ppsetApply .
.
probeMatch-methods .
probeNames-methods .
ProbeSet-class .
.
ProgressBarText-class .
.
read.affybatch .
.
.
read.probematrix .
.
.
.
rma
.
.
.
.
.
SpikeIn .
.
.
.
summary .
.
.
.
tukey.biweight .
.
whatcdf
.
.
.
.
.
.
xy2indices .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
.
.
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
.
Index
63
.setAffyOptions
~~function to set options ~~
Description
~~ Set the options for the package
Usage
.setAffyOptions(affy.opt = NA)
Arguments
affy.opt
A list structure of options. If NA, the default options are set.
Details
See the vignettes to know more. This function could disappear in favor of a more general one the
package Biobase.
Value
The function is used for its side effect. Nothing is returned.
Author(s)
Laurent
4
Examples
affy.opt <- getOption("BioC")$affy
.setAffyOptions(affy.opt)
affy-options
affy-deprecated
Deprecated functions in package ‘affy’
Description
These functions are provided for compatibility with older versions of affy only, and will be defunct
at the next release.
Details
The following functions are deprecated and will be made defunct; use the replacement indicated
below:
• loess.normalize: normalize.loess
• maffy.normalize
• multiloess
• simplemultiLoess
affy-options
Options for the affy package
Description
Description of the options for the affy package.
Note
The affy package options are contained in the Bioconductor options. The options are:
• use.widgets: a logical used to decide on the default of widget use.
• compress.cel: a logical
• compress.cdf: a logical
• probes.loc: a list. Each element of the list is it self a list with two elements what and where.
When looking for the informations about the locations of the probes on the array, the elements
in the list will be looked at one after the other. The first one for which what and where lead
to the matching locations information is used. The element what can be one of package,
environment or file. The element where depends on the corresponding element what.
– if package: location for the package (like it would be for the argument lib.loc for the
function library.)
– if environment: an environment to look for the information (like the argument env for
the function get).
– if file: a character with the path in which a CDF file can be found.
5
affy.scalevalue.exprSet
Examples
## get the options
opt <- getOption("BioC")
affy.opt <- opt$affy
## list their names
names(affy.opt)
## set the option compress.cel
affy.opt$compress.cel <- TRUE
options(BioC=opt)
affy.scalevalue.exprSet
Scale normalization for expreSets
Description
Normalizes expression values using the method described in the Affymetrix user manual.
Usage
affy.scalevalue.exprSet(eset, sc = 500, analysis="absolute")
Arguments
eset
sc
analysis
Details
An ExpressionSet object.
Value at which all arrays will be scaled to.
Should we do absolute or comparison analysis, although "comparison" is still
not implemented.
This is function was implemented from the Affymetrix technical documentation for MAS 5.0. It
can be downloaded from the website of the company. Please refer to this document for details.
Value
A normalized ExpressionSet.
Author(s)
Laurent
6
AffyBatch-class
AffyBatch-class
Class AffyBatch
Description
This is a class representation for Affymetrix GeneChip probe level data. The main component are
the intensities from multiple arrays of the same CDF type. It extends eSet.
Objects from the Class
Objects can be created using the function read.affybatch or the wrapper ReadAffy.
Slots
cdfName: Object of class character representing the name of CDF file associated with the arrays
in the AffyBatch.
nrow: Object of class integer representing the physical number of rows in the arrays.
ncol: Object of class integer representing the physical number of columns in the arrays.
assayData: Object of class AssayData containing the raw data, which will be at minimum a matrix
of intensity values. This slot can also hold a matrix of standard errors if the ’sd’ argument is
set to TRUE in the call to ReadAffy.
phenoData: Object of class AnnotatedDataFrame containing phenotypic data for the samples.
annotation A character string identifying the annotation that may be used for the ExpressionSet
instance.
protocolData: Object of class AnnotatedDataFrame containing protocol data for the samples.
featureData Object of class AnnotatedDataFrame containing feature-level (e.g., probeset-level)
information.
experimentData: Object of class "MIAME" containing experiment-level information.
.__classVersion__: Object of class Versions describing the R and Biobase version number used
to create the instance. Intended for developer use.
Extends
Class "eSet", directly.
Methods
cdfName signature(object = "AffyBatch"): obtains the cdfName slot.
pm<- signature(object = "AffyBatch"): replaces the perfect match intensities.
pm signature(object = "AffyBatch"): extracts the pm intensities.
mm<- signature(object = "AffyBatch"): replaces the mismatch intensities.
mm signature(object = "AffyBatch"): extracts the mm intensities.
AffyBatch-class
7
probes signature(object = "AffyBatch", which): extract the perfect match or mismatch
probe intensities. Uses which can be "pm" and "mm".
exprs signature(object = "AffyBatch"): extracts the expression matrix.
exprs<- signature(object = "AffyBatch", value = "matrix"): replaces the expression
matrix.
se.exprs signature(object = "AffyBatch"): extracts the matrix of standard errors of expres-
sion values, if available.
se.exprs<- signature(object = "AffyBatch", value = "matrix"): replaces the matrix of
standard errors of expression values.
[<- signature(x = "AffyBatch"): replaces subsets.
[ signature(x = "AffyBatch"): subsets by array.
boxplot signature(x = "AffyBatch"): creates a boxplots of log base 2 intensities (pm, mm or
both). Defaults to both.
hist signature(x = "AffyBatch"): creates a plot showing all the histograms of the pm,mm or
both data. See plotDensity.
computeExprSet signature(x = "AffyBatch",
summary.method = "character"): For
each probe set computes an expression value using summary.method.
featureNames signature(object = "AffyBatch"): return the probe set names also referred to
as the Affymetrix IDs. Notice that one can not assign featureNames. You must do this by
changing the cdfenvs.
geneNames signature(object="AffyBatch"): deprecated, use featureNames.
getCdfInfo signature(object = "AffyBatch"): retrieve the environment that defines the loca-
tion of probes by probe set.
image signature(x = "AffyBatch"): creates an image for each sample.
indexProbes signature(object = "AffyBatch", which = "character"): returns a list with
locations of the probes in each probe set. The affyID corresponding to the probe set to retrieve
can be specified in an optional parameter genenames. By default, all the affyIDs are retrieved.
The names of the elements in the list returned are the affyIDs. which can be "pm", "mm", or
"both". If "both" then perfect match locations are given followed by mismatch locations.
signature(object = "AffyBatch", which = "missing") (i.e., calling indexProbes
without a "which" argument) is the same as setting "which" to "pm".
intensity<- signature(object = "AffyBatch"): a replacement method for the exprs slot, i.e.
the intensities.
intensity signature(object = "AffyBatch"): extract the exprs slot, i.e. the intensities.
length signature(x = "AffyBatch"): returns the number of samples.
pmindex signature(object = "AffyBatch"): return the location of perfect matches in the
intensity matrix.
mmindex signature(object = "AffyBatch"): return the location of the mismatch intensities.
dim signature(x = "AffyBatch"): Row and column dimensions.
ncol signature(x = "AffyBatch"): An accessor function for ncol.
nrow signature(x = "AffyBatch"): an accessor function for nrow.
8
AffyBatch-class
normalize signature(object = "AffyBatch"): a method to normalize. The method accepts an
argument method. The default methods is specified in package options (see the main vignette).
normalize.methods signature(object = "AffyBatch"): returns the normalization methods
defined for this class. See normalize.
probeNames signature(object = "AffyBatch"): returns the probe set associated with each
row of the intensity matrix.
probeset signature(object = "AffyBatch",genenames=NULL,
locations=NULL): Extracts
ProbeSet objects related to the probe sets given in genenames. If an alternative set of loca-
tions defining pms and mms a list with those locations should be passed via the locations
argument.
bg.correct signature(object = "AffyBatch",
correction methods defined by method.
method="character") applies background
updateObject signature(object = "AffyBatch", ...,
verbose=FALSE): update, if nec-
essary, an object of class AffyBatch to its current class definition. verbose=TRUE provides
details about the conversion process.
Note
This class is better described in the vignette.
See Also
related methods merge.AffyBatch, pairs.AffyBatch, and eSet
Examples
if (require(affydata)) {
## load example
data(Dilution)
## nice print
print(Dilution)
pm(Dilution)[1:5,]
mm(Dilution)[1:5,]
## get indexes for the PM probes for the affyID "1900_at"
mypmindex <- pmindex(Dilution,"1900_at")
## same operation using the primitive
mypmindex <- indexProbes(Dilution, which="pm", genenames="1900_at")[[1]]
## get the probe intensities from the index
intensity(Dilution)[mypmindex, ]
description(Dilution) ##we can also use the methods of eSet
sampleNames(Dilution)
abstract(Dilution)
}
相关推荐
2023年江西萍乡中考道德与法治真题及答案.doc
2012年重庆南川中考生物真题及答案.doc
2013年江西师范大学地理学综合及文艺理论基础考研真题.doc
2020年四川甘孜小升初语文真题及答案I卷.doc
2020年注册岩土工程师专业基础考试真题及答案.doc
2023-2024学年福建省厦门市九年级上学期数学月考试题及答案.doc
2021-2022学年辽宁省沈阳市大东区九年级上学期语文期末试题及答案.doc
2022-2023学年北京东城区初三第一学期物理期末试卷及答案.doc
2018上半年江西教师资格初中地理学科知识与教学能力真题及答案.doc
2012年河北国家公务员申论考试真题及答案-省级.doc
2020-2021学年江苏省扬州市江都区邵樊片九年级上学期数学第一次质量检测试题及答案.doc
2022下半年黑龙江教师资格证中学综合素质真题及答案.doc
