simpleaffy: Very simple high level analysis of Affymetrix data

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...

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("simpleaffy")
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)
Version2.50.0
http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/

View on Bioconductor

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

all.present Man page
all.present.in.group Man page
arrayType Man page
arrayType-method Man page
arrayType,QCStats-method Man page
avbg Man page
avbg-method Man page
avbg,QCStats-method Man page
bg.correct.sa Man page
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
detection.p.val Man page
fc Man page
fc,PairComp-method Man page
getActin3 Man page
getActin5 Man page
getActinM Man page
getAllQCProbes Man page
getAllSpikeProbes Man page
getAlpha1 Man page
getAlpha2 Man page
get.annotation Man page
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 Man page
get.array.subset,AffyBatch-method Man page
get.array.subset,ExpressionSet-method Man page
get.array.subset.exprset Man page
getBioB Man page
getBioC Man page
getBioD Man page
getCreX Man page
get.fold.change.and.t.test Man page
getGapdh3 Man page
getGapdh5 Man page
getGapdhM Man page
getTao Man page
group Man page
group,PairComp-method Man page
haveQCParams Man page
hmap.eset Man page
hmap.pc Man page
journalpng Man page
justMAS Man page
maxbg Man page
maxbg-method Man page
maxbg,QCStats-method Man page
means Man page
means,PairComp-method Man page
members Man page
members,PairComp-method Man page
minbg Man page
minbg-method Man page
minbg,QCStats-method Man page
PairComp-class Man page
[<-,PairComp-method Man page
[,PairComp-method Man page
pairwise.comparison Man page
pairwise.filter Man page
pairwise.filter,PairComp-method Man page
pData Man page
pData,PairComp-method Man page
percent.present Man page
percent.present-method Man page
percent.present,QCStats-method Man page
plot,PairComp Man page
plot,PairComp,ANY-method Man page
plot,PairComp-method Man page
plot,PairComp,missing-method Man page
plot,PairComp,PairComp-method Man page
plot.pairwise.comparison Man page
plot.qc.stats Man page
plot,QCStats Man page
plot,QCStats,ANY-method Man page
plot,QCStats,missing-method Man page
qc Man page
qc.add.probe Man page
qc.add.ratio Man page
qc.add.spike Man page
qc.affy Man page
qc,AffyBatch-method Man page
qc.get.alpha1 Man page
qc.get.alpha2 Man page
qc.get.array 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.have.params Man page
qc.ok Man page
qcProbes Man page
qcProbes-method Man page
qcProbes,QCStats-method Man page
qc.read.file Man page
qcs Man page
qc.set.alpha1 Man page
qc.set.alpha2 Man page
qc.set.array Man page
QCStats-class Man page
ratios Man page
ratios-method Man page
ratios,QCStats-method Man page
read.affy Man page
read.affy.mixed Man page
red.black.green.cols Man page
red.yellow.white.cols Man page
results.summary Man page
screenpng Man page
setQCEnvironment Man page
sfs Man page
sfs-method Man page
sfs,QCStats-method Man page
simpleaffy-deprecated Man page
spikeInProbes Man page
spikeInProbes-method Man page
spikeInProbes,QCStats-method Man page
standard.pearson Man page
target Man page
target-method Man page
target,QCStats-method Man page
trad.scatter.plot Man page
tt Man page
tt,PairComp-method Man page
write.annotation Man page

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

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