Package: affyPLM 1.83.2

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]>

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affyPLM.pdf |affyPLM.html✨
affyPLM/json (API)

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

Peer review:

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

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

On BioConductor:affyPLM-1.83.2(bioc 3.21)affyPLM-1.82.0(bioc 3.20)

microarrayonechannelpreprocessingqualitycontrolopenblaszlib

6.76 score 4 packages 204 scripts 1.6k downloads 162 mentions 61 exports 25 dependencies

Last updated 7 days agofrom:38ee0fa4e8. Checks:ERROR: 2 WARNING: 7. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 19 2024
R-4.5-win-x86_64WARNINGNov 29 2024
R-4.5-linux-x86_64ERRORDec 19 2024
R-4.4-win-x86_64WARNINGNov 29 2024
R-4.4-mac-x86_64WARNINGDec 19 2024
R-4.4-mac-aarch64WARNINGDec 19 2024
R-4.3-win-x86_64WARNINGNov 29 2024
R-4.3-mac-x86_64WARNINGDec 19 2024
R-4.3-mac-aarch64WARNINGDec 19 2024

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:affyaffyioaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlgcrmagenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVectorzlibbioc

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