simpleaffy: Very simple high level analysis of Affymetrix data
Version 2.52.0

Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...

AuthorCrispin J Miller
Bioconductor views Annotation DataImport DifferentialExpression Microarray OneChannel Preprocessing QualityControl ReportWriting Transcription Visualization
Date of publicationNone
MaintainerCrispin Miller <cmiller@picr.man.ac.uk>
LicenseGPL (>= 2)
Version2.52.0
URL http://www.bioconductor.org http://bioinformatics.picr.man.ac.uk/simpleaffy/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("simpleaffy")

Popular man pages

get.array.subset.affy: Get a subset of arrays from an affybatch object, split by...
get.fold.change.and.t.test: Compute fold change and t-test statistics between two...
journalpng: Produce a device for producing artwork for presentations and...
PairComp-class: Class "PairComp" Represents the results of pairwise...
pairwise.filter: Filter pairwise comparison statistics between two...
qc.stats: an example QC Stats object
QCStats-class: Class "QCStats"
See all...

All man pages Function index File listing

Man pages

all.present: Filter by PMA call
all.present.in.group: Filter by PMA call
bg.correct.sa: Simpleaffy Implementation of Mas5 Background Correction
call.exprs: Generate Expression Summaries for Affymetrix Data
detection.p.val: Calculate Detection p-values
get.annotation: Get annotation data for a gene list
get.array.indices: Find arrays in an AffyBatch object defined by their phenoData
get.array.subset: Get a subset of arrays from an affybatch object, split by...
get.array.subset.affy: Get a subset of arrays from an affybatch object, split by...
get.fold.change.and.t.test: Compute fold change and t-test statistics between two...
hmap.colors: Generate colourings for heatmaps
hmap.eset: Draw a heatmap from an AffyBatch object
hmap.pc: Draw a heatmap from an PairComp object
journalpng: Produce a device for producing artwork for presentations and...
justMAS: Generate Expression calls using a C implementation of the MAS...
PairComp-class: Class "PairComp" Represents the results of pairwise...
pairwise.comparison: Compute pairwise comparison statistics between two...
pairwise.filter: Filter pairwise comparison statistics between two...
plot.pairwise.comparison: Plots a PairComp object
plot.qc.stats: Plots a QCStats object
qc: Generate QC stats from an AffyBatch object
qc.affy: Generate Affymetrix Style QC Statistics
qc.get.alpha1: Get or set the alpha values for the current QC environment
qc.get.array: Get or set the name of the array for which the current QC...
qc.get.probes: Retrieve QC probeset names for the current array type
qc.get.ratios: Retrieve pairs of probesets used for calculating 3'/5' ratios
qc.get.spikes: Retrieve QC spike probeset names for the current array type
qc.have.params: Does simpleaffy have a QC definition file for the specified...
qc.ok: Has simpleaffy's QC environment been set up?
qc.read.file: Read a file defining the QC parameters for a specified array...
qc.stats: an example QC Stats object
QCStats-class: Class "QCStats"
read.affy: Read a Set of .CEL Files and Phenotypic Data
read.affy.mixed: Read a Set of .CEL Files and Phenotypic Data from mixed chip...
setQCEnvironment: Establish the appropriate QC environment for the specified...
simpleaffy-deprecated: Does simpleaffy have a QC definition file for the specified...
standard.pearson: A clustering function based on pearson correlation
trad.scatter.plot: Does a Traditional Scatter Plot of Expression Data

Functions

qc.add.probe Man page
qc.add.ratio Man page
qc.add.spike Man page
qc.get.alpha1 Man page
qc.get.alpha2 Man page
qc.get.probe Man page
qc.get.probes Man page
qc.get.ratio Man page
qc.get.ratios Man page
qc.get.spike Man page
qc.get.spikes Man page
qc.get.tau Man page
qc.set.alpha1 Man page
qc.set.alpha2 Man page
qc.have.params Man page
qc.ok Man page
qc.read.file Man page
simpleaffy-deprecated Man page
PairComp-class Man page
QCStats-class Man page
[,PairComp-method Man page
[<-,PairComp-method Man page
all.present Man page Source code
all.present.in.group Man page Source code
arrayType Man page
arrayType,QCStats-method Man page
arrayType-method Man page
avbg Man page
avbg,QCStats-method Man page
avbg-method Man page
bg.correct.sa Man page Source code
bg.stats Source code
blue.white.red.cols Man page
calculated.from Man page
calculated.from,PairComp-method Man page
call.exprs Man page
calls Man page
calls,PairComp-method Man page
createEmptyQCEnvironment Source code
detection.p.val Man page Source code
f.probeset.not.found Source code
fc Man page
fc,PairComp-method Man page
get.annotation Man page Source code
get.array.def.file Source code
get.array.indices Man page
get.array.indices,AffyBatch-method Man page
get.array.indices,ExpressionSet-method Man page
get.array.subset Man page
get.array.subset,AffyBatch-method Man page
get.array.subset,ExpressionSet-method Man page
get.array.subset.affybatch Man page
get.array.subset.exprset Man page
get.fold.change.and.t.test Man page
getActin3 Man page Source code
getActin5 Man page Source code
getActinM Man page Source code
getAllQCProbes Man page Source code
getAllSpikeProbes Man page Source code
getAlpha1 Man page Source code
getAlpha2 Man page Source code
getBioB Man page Source code
getBioC Man page Source code
getBioD Man page Source code
getCreX Man page Source code
getGapdh3 Man page Source code
getGapdh5 Man page Source code
getGapdhM Man page Source code
getRatios Source code
getTao Man page Source code
group Man page
group,PairComp-method Man page
haveQCParams Man page Source code
hmap.eset Man page Source code
hmap.pc Man page Source code
journalpng Man page Source code
justMAS Man page Source code
maplot Source code
mas5 Source code
maxbg Man page
maxbg,QCStats-method Man page
maxbg-method Man page
means Man page
means,PairComp-method Man page
members Man page
members,PairComp-method Man page
minbg Man page
minbg,QCStats-method Man page
minbg-method Man page
nitializeQCEnvironment Source code
pData Man page
pData,PairComp-method Man page
pairwise.comparison Man page
pairwise.filter Man page Source code
pairwise.filter,PairComp-method Man page
pcscatterplot Source code
percent.present Man page
percent.present,QCStats-method Man page
percent.present-method Man page
plot,PairComp Man page
plot,PairComp,ANY-method Man page
plot,PairComp,PairComp-method Man page
plot,PairComp,missing-method Man page
plot,PairComp-method Man page
plot,QCStats Man page
plot,QCStats,ANY-method Man page
plot,QCStats,missing-method Man page
plot.pairwise.comparison Man page Source code
plot.qc.stats Man page Source code
qc Man page
qc,AffyBatch-method Man page
qc.add.probe Source code
qc.add.ratio Source code
qc.add.spike Source code
qc.affy Man page Source code
qc.file.addQCRatio Source code
qc.file.addQCSpike Source code
qc.file.setAlpha1 Source code
qc.file.setAlpha2 Source code
qc.file.setQCArray Source code
qc.get.alpha1 Source code
qc.get.alpha2 Source code
qc.get.array Man page Source code
qc.get.probe Source code
qc.get.probes Source code
qc.get.ratio Source code
qc.get.ratios Source code
qc.get.spike Source code
qc.get.spikes Source code
qc.get.tau Source code
qc.have.params Source code
qc.is.empty Source code
qc.ok Source code
qc.read.file Source code
qc.set.alpha1 Source code
qc.set.alpha2 Source code
qc.set.array Man page Source code
qc.set.empty Source code
qc.test Source code
qcProbes Man page
qcProbes,QCStats-method Man page
qcProbes-method Man page
qcs Man page
ratios Man page
ratios,QCStats-method Man page
ratios-method Man page
read.affy Man page Source code
read.affy.mixed Man page
red.black.green.cols Man page
red.yellow.white.cols Man page
results.summary Man page Source code
screenpng Man page Source code
setQCEnvironment Man page Source code
sfs Man page
sfs,QCStats-method Man page
sfs-method Man page
spikeInProbes Man page
spikeInProbes,QCStats-method Man page
spikeInProbes-method Man page
standard.pearson Man page Source code
strip.list Source code
target Man page
target,QCStats-method Man page
target-method Man page
trad.scatter.plot Man page
tt Man page
tt,PairComp-method Man page
volcanoplot Source code
write.annotation Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/call.exprs.R
R/detection.p.val.R
R/get.annotation.R
R/heatmap.R
R/justMAS.R
R/pairwise.comparison.R
R/qc.stats.R
R/read.affy.R
R/trad.scatter.plot.R
README
build
build/vignette.rds
data
data/qcs.rda
inst
inst/doc
inst/doc/simpleAffy.R
inst/doc/simpleAffy.Rnw
inst/doc/simpleAffy.pdf
inst/extdata
inst/extdata/atgenomecdf.qcdef
inst/extdata/ath1121501cdf.qcdef
inst/extdata/celeganscdf.qcdef
inst/extdata/drosgenome1cdf.qcdef
inst/extdata/hcg110cdf.qcdef
inst/extdata/hgfocuscdf.qcdef
inst/extdata/hgu133a2cdf.qcdef
inst/extdata/hgu133acdf.qcdef
inst/extdata/hgu133atagcdf.qcdef
inst/extdata/hgu133bcdf.qcdef
inst/extdata/hgu133plus2cdf.qcdef
inst/extdata/hgu95acdf.qcdef
inst/extdata/hgu95av2cdf.qcdef
inst/extdata/hgu95bcdf.qcdef
inst/extdata/hgu95ccdf.qcdef
inst/extdata/hgu95dcdf.qcdef
inst/extdata/hgu95ecdf.qcdef
inst/extdata/mgu74acdf.qcdef
inst/extdata/mgu74av2cdf.qcdef
inst/extdata/mgu74bcdf.qcdef
inst/extdata/mgu74bv2cdf.qcdef
inst/extdata/mgu74ccdf.qcdef
inst/extdata/mgu74cv2cdf.qcdef
inst/extdata/moe430acdf.qcdef
inst/extdata/mouse4302cdf.qcdef
inst/extdata/mouse430a2cdf.qcdef
inst/extdata/mouse430b2cdf.qcdef
inst/extdata/mu11ksubacdf.qcdef
inst/extdata/mu11ksubbcdf.qcdef
inst/extdata/poplarcdf.qcdef
inst/extdata/porcinecdf.qcdef
inst/extdata/rae230acdf.qcdef
inst/extdata/rae230bcdf.qcdef
inst/extdata/rat2302cdf.qcdef
inst/extdata/rgu34acdf.qcdef
inst/extdata/rgu34bcdf.qcdef
inst/extdata/rgu34ccdf.qcdef
inst/extdata/rhesuscdf.qcdef
inst/extdata/soybeancdf.qcdef
inst/extdata/vitisviniferacdf.qcdef
inst/extdata/yeast2cdf.qcdef
inst/extdata/ygs98cdf.qcdef
inst/extdata/zebrafishcdf.qcdef
man
man/PairComp-class.Rd
man/QCStats-class.Rd
man/all.present.Rd
man/all.present.in.group.Rd
man/bg.correct.sa.Rd
man/call.exprs.Rd
man/detection.p.val.Rd
man/get.annotation.Rd
man/get.array.indices.Rd
man/get.array.subset.Rd
man/get.array.subset.affy.Rd
man/get.fold.change.and.t.test.Rd
man/hmap.colors.Rd
man/hmap.eset.Rd
man/hmap.pc.Rd
man/journalpng.Rd
man/justMAS.Rd
man/pairwise.comparison.Rd
man/pairwise.filter.Rd
man/plot.pairwise.comparison.Rd
man/plot.qc.stats.Rd
man/qc.Rd
man/qc.affy.Rd
man/qc.get.alpha1.Rd
man/qc.get.array.Rd
man/qc.get.probes.Rd
man/qc.get.ratios.Rd
man/qc.get.spikes.Rd
man/qc.have.params.Rd
man/qc.ok.Rd
man/qc.read.file.Rd
man/qc.stats.Rd
man/read.affy.Rd
man/read.affy.mixed.Rd
man/setQCEnvironment.Rd
man/simpleaffy-deprecated.Rd
man/standard.pearson.Rd
man/trad.scatter.plot.Rd
src
src/simpleaffy.c
vignettes
vignettes/QCandSimpleaffy.pdf
vignettes/simpleAffy.Rnw
simpleaffy documentation built on May 20, 2017, 9:44 p.m.

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