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xps (version 1.32.0)

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

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Version

Version

1.32.0

License

GPL (>= 2.0)

Maintainer

Christian Stratowa

Last Published

February 15th, 2017

Functions in xps (1.32.0)

callFilter-methods

Detection Call Filter

boxplot-methods

cvFilter-methods

Coefficient of Variation Filter

Detection Above Background Call

attachInten-methods

Attach/Remove Intensities

coiplot-methods

Center-Of-Intensity QC Plots

attachMask-methods

Attach/Remove Scheme Mask

corplot-methods

Array-Array Expression Level Correlation Plot

Factor Analysis for Robust Microarray Summarization Expression Measure

attachUnitNames-methods

Attach/Remove Unit Names

attachDataXY-methods

Attach/Remove (X,Y)-Coordinates

attachExpr-methods

Attach/Remove Expression Measures

attachProbe-methods

Attach/Remove Probe Sequence and/or GC Content

Test for Existing ROOT File

diffFilter-methods

Difference Filter

Functions to assess RNA Degradation.

addData-methods

Import additional CEL files into a DataTreeSet

Base Class Filter

Export data as text files

FilterTreeSet-class

Class FilterTreeSet

Get Probe Information

Get Number of Trees

MAS 5.0 Expression Measure

Plot Density Estimate for Device

mboxplot-methods

Box Plots of Relative M Values

Plot Image(s) for Device

fcFilter-methods

Fold-Change Filter

PreFilter-constructor

Constructor for Class PreFilter

Get Chip Name and Type

madFilter-methods

Median Absolute Deviation Filter

highFilter-methods

Upper Threshold Filter

Plot Density Estimate

Export data from ROOT file

import.exon.scheme

Import CLF, PGF and annotation files into a SchemeTreeSet

MAS 4.0 Expression Measure

import.expr.scheme

Import CDF, probe and annotation files into a SchemeTreeSet

MAS 5.0 Absolute Detection Call

Normalized Unscaled Standard Errors (NUSE)

Get Expression Levels from FIRMA

Finding Isoforms using Robust Multichip Analysis

Get Splice Score from FIRMA

Functions for fitting probe-level models

indexUnits-methods

import.genome.scheme

Import CLF, PGF and annotation files into a SchemeTreeSet

Informative/Non-Informative Call

initialize-methods

Initialize Classes

pcaplot-methods

Plots of Border Elements for Device

Center-Of-Intensity QC Plots for Device

attachCall-methods

Attach/Remove Detecion Call Measures

Array-Array Expression Level Correlation Plot for Device

attachData-methods

Attach/Remove Data

callplot-methods

Barplot of Percent Present and Absent Calls.

CallTreeSet-class

Class CallTreeSet

Conversion of Parameter exonlevel to Integer

Export filter data as text files

ExprTreeSet-class

Class ExprTreeSet

madplot-methods

Array-Array Expression Level Distance Plot

Get Tree Names w/o Extension

Array-Array Expression Level Distance Plot for Device

Normalization on Affymetrix Probe Level Data or on Expression Levels

Box Plots of Normalized Unscaled Standard Errors (NUSE) for Device

Plot of Probe Intensities for a Probeset for Device.

Box Plots of Relative Log Expression (RLE) for Device

ProjectInfo-class

Class ProjectInfo

AnalysisTreeSet-class

Class AnalysisTreeSet

Methods for accessing perfect matches and mismatches

quantileFilter-methods

Quantile Filter

Probe Set Quality Control Functions

QualTreeSet-class

Class QualTreeSet

ratioFilter-methods

Create class ExprTreeSet accessing ROOT expression file

PCA Plot for Device

nuseplot-methods

Box Plots of Normalized Unscaled Standard Errors (NUSE)

Barplot of PM and MM Intensities for Device

rleplot-methods

Box Plots of Relative Log Expression (RLE)

Robust Multi-Array Average Expression Measure

attachBgrd-methods

Attach/Remove Background Intensities

root.merge.data

Create class DataTreeSet by merging ROOT data files

Background Correction

borderplot-methods

Plots of Border Elements

DataTreeSet-class

Class DataTreeSet

Distribution Free Weighted Expression Measure

Compute expression levels from raw data

Functions for fitting RMA as probe-level model

Get Extension of Tree Names

gapFilter-methods

getTreeData-methods

Export Tree Data

Test for ROOT File

lowFilter-methods

Lower Threshold Filter

ROOT Profile Plot

Create class SchemeTreeSet accessing ROOT scheme file

Get/Set Expression Values

Display an Image

Import CEL files into a DataTreeSet

Function for Applying a PreFilter to an ExprTreeSet

probeContentGC-methods

Get G/C Content for Probes

intensity-methods

Get/Set Data Values

presCall-methods

Get/Set Present Call Values

root.browser-methods

Open the ROOT object browser

Create class CallTreeSet accessing ROOT detection call file

ROOT An Object-Oriented Data Analysis Framework

transposed Robust Multi-Array Average Expression Measure

varFilter-methods

Variance Filter

Validate Tree Type

xps Package Overview

volcanoplot-methods

ROOT M vs A Plot

SchemeTreeSet-class

Class SchemeTreeSet

Probe Set Summarizing Functions

UniFilter-constructor

Constructor for Class UniFilter

Function for Applying an UniFilter to an ExprTreeSet

ProjectInfo-constructor

Constructor for Class ProjectInfo

ROOT 2D-Histogram

ROOT 3D-Histogram

validSE-methods

Get Valid Standard Errors

validExpr-methods

Get Valid Expression Levels

intensity2GCplot-methods

Boxlot of Probe Intensities Stratified by GC Content.

Create MetaProbeset File for APT

plotIntensity2GC

Boxlot of Probe Intensities Stratified by GC Content for Device.

mvaplot-methods

probeSequence-methods

Get Probe Sequence

MvA Scatter Plot for Device

probesetID2unitID-methods

Conversion between Probeset IDs and UnitIDs

Create class DataTreeSet accessing ROOT data file

UniFilter-class

Class UniFilter

Convert Method Type to Tree Extension

ROOT Density Plot

uniTest-methods

A Two-Group Unitest

unitestFilter-methods

Create Quality Assessment Report.

Box Plots for Device

Barplot of Percent Present and Absent Calls for Device

Barplot of PM and MM Intensities.

PreFilter-class

Class PreFilter

probesetplot-methods

Plot of Probe Intensities for a Probeset.

ProcesSet-class

Class ProcesSet

rawCELName-methods

Method for getting names of the raw CEL-files

Relative Log Expression (RLE)

ROOT 1D-Histogram

symbol2unitID-methods

Conversion between Gene Symbols and UnitIDs

treeInfo-methods

Get UserInfo from ROOT Trees

validCall-methods

Get Valid Detection Call Values

validData-methods

Extract Subset of Data