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...

AuthorCrispin J Miller
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

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

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