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...

Author
Crispin J Miller
Date of publication
None
Maintainer
Crispin Miller <cmiller@picr.man.ac.uk>
License
GPL (>= 2)
Version
2.50.0
URLs

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

Files in this package

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