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simpleaffy (version 2.48.0)

Very simple high level analysis of Affymetrix data

Description

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...

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Version

Version

2.48.0

License

GPL (>= 2)

Maintainer

Crispin Miller

Last Published

February 15th, 2017

Functions in simpleaffy (2.48.0)

qc

Generate QC stats from an AffyBatch object
qc.get.array

Get or set the name of the array for which the current QC environment is valid. Currently not used for anything important; is a free text identifier.
call.exprs

Generate Expression Summaries for Affymetrix Data
plot.pairwise.comparison

Plots a PairComp object
detection.p.val

Calculate Detection p-values
hmap.eset

Draw a heatmap from an AffyBatch object
get.array.subset.affybatch

Get a subset of arrays from an affybatch object, split by phnotypic data
justMAS

Generate Expression calls using a C implementation of the MAS 5.0 Algorithm
qc.affy

Generate Affymetrix Style QC Statistics
all.present.in.group

Filter by PMA call
all.present

Filter by PMA call
PairComp-class

Class "PairComp" Represents the results of pairwise comparison between two experimental factors
get.array.subset

Get a subset of arrays from an affybatch object, split by phnotypic data
qc.ok

Has simpleaffy's QC environment been set up?
qc.get.alpha1

Get or set the alpha values for the current QC environment
bg.correct.sa

Simpleaffy Implementation of Mas5 Background Correction
pairwise.filter

Filter pairwise comparison statistics between two experimental groups
pairwise.comparison

Compute pairwise comparison statistics between two experimental groups
plot.qc.stats

Plots a QCStats object
get.array.indices

Find arrays in an AffyBatch object defined by their phenoData
standard.pearson

A clustering function based on pearson correlation
QCStats-class

Class "QCStats"
qc.get.probes

Retrieve QC probeset names for the current array type
get.fold.change.and.t.test

Compute fold change and t-test statistics between two experimental groups
get.annotation

Get annotation data for a gene list
read.affy.mixed

Read a Set of .CEL Files and Phenotypic Data from mixed chip types
qc.get.ratios

Retrieve pairs of probesets used for calculating 3'/5' ratios
trad.scatter.plot

Does a Traditional Scatter Plot of Expression Data
blue.white.red.cols

Generate colourings for heatmaps
qc.get.spikes

Retrieve QC spike probeset names for the current array type
read.affy

Read a Set of .CEL Files and Phenotypic Data
qc.read.file

Read a file defining the QC parameters for a specified array and set up the QC Environment
journalpng

Produce a device for producing artwork for presentations and journals
hmap.pc

Draw a heatmap from an PairComp object
qcs

an example QC Stats object
qc.have.params

Does simpleaffy have a QC definition file for the specified array?
setQCEnvironment

Establish the appropriate QC environment for the specified array
simpleaffy-deprecated

Does simpleaffy have a QC definition file for the specified array?
qc.get.probes

Retrieve QC probeset names for the current array type
qc.have.params

Does simpleaffy have a QC definition file for the specified array?
qc.ok

Has simpleaffy's QC environment been set up?
qc.read.file

Read a file defining the QC parameters for a specified array and set up the QC Environment
qc.get.alpha1

Get or set the alpha values for the current QC environment
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
simpleaffy-deprecated

Does simpleaffy have a QC definition file for the specified array?