Package: affyPLM 1.89.0

Ben Bolstad

affyPLM: Methods for fitting probe-level models

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

Authors:Ben Bolstad <[email protected]>

affyPLM_1.89.0.tar.gz
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affyPLM_1.89.0.tgz(r-4.6-x86_64)affyPLM_1.89.0.tgz(r-4.6-arm64)affyPLM_1.89.0.tgz(r-4.5-x86_64)affyPLM_1.89.0.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
affyPLM/json (API)

# Install 'affyPLM' in R:
install.packages('affyPLM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bmbolstad/affyplm/issues

Uses libs:
  • openblas– Optimized BLAS
  • zlib– Compression library

On BioConductor:affyPLM-1.89.0(bioc 3.24)affyPLM-1.88.0(bioc 3.23)

microarrayonechannelpreprocessingqualitycontrolopenblaszlib

8.06 score 4 packages 239 scripts 162 mentions 61 exports 14 dependencies

Last updated from:31ba047388. Checks:1 ERROR, 7 WARNING, 5 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR194
linux-devel-arm64WARNING246
linux-devel-x86_64WARNING306
source / vignettesOK275
linux-release-arm64WARNING244
linux-release-x86_64WARNING277
macos-release-arm64OK198
macos-release-x86_64OK372
macos-oldrel-arm64OK211
macos-oldrel-x86_64OK451
windows-develWARNING567
windows-releaseWARNING566
windows-oldrelWARNING537
wasm-releaseFAIL234

Exports:bg.correct.gcrmabg.correct.LESNbg.correct.shiftbg.correct.stretchboxplotcoefscoefs.constcoefs.probecoefs<-convert.LESN.paramfitPLMget.background.codeget.default.psi.kget.normalization.codeget.psi.codeget.summary.codehistindexProbesProcessedmodel.descriptionnormalize.AffyBatch.quantiles.chromosomenormalize.AffyBatch.quantiles.probesetnormalize.AffyBatch.scalingnormalize.ExpressionSet.contrastsnormalize.ExpressionSet.invariantsetnormalize.ExpressionSet.loessnormalize.ExpressionSet.methodsnormalize.ExpressionSet.qsplinenormalize.ExpressionSet.quantilesnormalize.ExpressionSet.scalingnormalize.scalingnormvecnuseNUSEPLM.designmatrix3PLMset2exprSetpreprocesspset2esetpseudoColorBarpseudoPaletteReadRMAExpressresidresid<-residSEresiduals<-RLErmaPLMsese.constse.probese<-summarythreestepthreestepPLMvarcovverify.bg.paramverify.constraint.typesverify.model.paramverify.norm.paramverify.output.paramverify.variable.typesweights<-

Dependencies:affyaffyioBiobaseBiocGenericsBiocManagerBiostringscrayongcrmagenericsIRangespreprocessCoreS4VectorsSeqinfoXVector

affyPLM: Advanced use of the MAplot function
Introduction | Basic Usage of the MAplot function | Gaining greater control over the function | Advanced Usage | Special notes about differences in MAplot for AffyBatch, ExpressionSet and PLMset objects. | Final Comments
Rendered fromMAplots.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

affyPLM: Fitting Probe Level Models
Introduction | Fitting Probe Level Models | How long will it take to run the model fitting procedures? | Dealing with the PLMset object | M-estimation: How fitPLM fits models | Variance Matrix and Standard error estimates for fitPLM
Rendered fromAffyExtensions.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

affyPLM: Model Based QC Assessment of Affymetrix GeneChips
Introduction | Fitting Probe Level Models for Quality Assessment | Quality Diagnostics | Final Comments
Rendered fromQualityAssess.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

affyPLM: the threestep function
Introduction | Using the threestep function | Methods available in threestep
Rendered fromThreeStep.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
LESN - Low End Signal is Noise Background correctionsbg.correct.LESN
Fit a Probe Level Model to Affymetrix Genechip Data.fitPLM
Relative M vs. A plotsMAplot MAplot,PLMset-method
Normalization applied to ExpressionSetsnormalize.ExpressionSet.contrasts normalize.ExpressionSet.invariantset normalize.ExpressionSet.loess normalize.ExpressionSet.methods normalize.ExpressionSet.qspline normalize.ExpressionSet.quantiles normalize.ExpressionSet.scaling
Quantile Normalization applied to probesetsnormalize.AffyBatch.quantiles.probeset
Scaling normalizationnormalize.AffyBatch.scaling normalize.scaling
Class PLMsetannotation,PLMset-method boxplot,PLMset-method cdfName,PLMset-method coefs coefs,PLMset-method coefs.const coefs.const,PLMset-method coefs.probe coefs.probe,PLMset-method coefs<- coefs<-,PLMset-method description,PLMset-method getCdfInfo,PLMset-method image,PLMset-method indexProbes,PLMset,character-method indexProbesProcessed indexProbesProcessed,PLMset-method Mbox Mbox,PLMset-method model.description model.description,PLMset-method normvec normvec,PLMset-method NUSE nuse NUSE,PLMset-method nuse,PLMset-method pData,PLMset-method pData<-,PLMset,data.frame-method phenoData,PLMset-method phenoData<-,PLMset,AnnotatedDataFrame-method PLMset PLMset-class resid resid,PLMset-method resid<- resid<-,PLMset-method residSE residSE,PLMset-method residuals residuals,PLMset-method residuals<- residuals<-,PLMset-method RLE RLE,PLMset-method sampleNames,PLMset-method sampleNames<- sampleNames<-,PLMset,character-method se se,PLMset-method se.const se.const,PLMset-method se.probe se.probe,PLMset-method se<- se<-,PLMset-method show,PLMset-method summary,PLMset-method varcov varcov,PLMset-method weights weights,PLMset-method weights<- weights<-,PLMset-method
Convert a PLMset to an ExpressionSetPLMset2exprSet pset2eset
Background correct and Normalizepreprocess
Coloring pseudo chip imagespseudoColorBar pseudoPalette
Read RMAExpress computed expression valuesReadRMAExpress
Fit a RMA to Affymetrix Genechip Data as a PLMsetrmaPLM
Three Step expression measuresthreestep
Three Step expression measures returned as a PLMsetthreestepPLM