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.

AuthorBen Bolstad <bmb@bmbolstad.com>
Date of publicationNone
MaintainerBen Bolstad <bmb@bmbolstad.com>
LicenseGPL (>= 2)
Version1.50.0
https://github.com/bmbolstad/affyPLM

View on Bioconductor

Functions

annotation,PLMset-method Man page
bg.correct.gcrma Man page
bg.correct.LESN Man page
bg.correct.shift Man page
bg.correct.stretch Man page
boxplot,PLMset-method Man page
cdfName,PLMset-method Man page
coefs Man page
coefs<- Man page
coefs.const Man page
coefs.const,PLMset-method Man page
coefs<-,PLMset-method Man page
coefs,PLMset-method Man page
coefs.probe Man page
coefs.probe,PLMset-method Man page
convert.LESN.param Man page
description,PLMset-method Man page
fitPLM Man page
fitPLM.old Man page
get.background.code Man page
getCdfInfo,PLMset-method Man page
get.default.psi.k Man page
get.normalization.code Man page
get.psi.code Man page
get.summary.code Man page
image,PLMset-method Man page
indexProbes,PLMset,character-method Man page
indexProbesProcessed Man page
indexProbesProcessed,PLMset-method Man page
MAplot Man page
MAplot,PLMset-method Man page
Mbox Man page
Mbox,PLMset-method Man page
model.description Man page
model.description,PLMset-method Man page
normalize.AffyBatch.quantiles.chromosome Man page
normalize.AffyBatch.quantiles.probeset Man page
normalize.AffyBatch.scaling Man page
normalize.ExpressionSet.contrasts Man page
normalize.ExpressionSet.invariantset Man page
normalize.ExpressionSet.loess Man page
normalize.ExpressionSet.methods Man page
normalize.ExpressionSet.qspline Man page
normalize.ExpressionSet.quantiles Man page
normalize.ExpressionSet.scaling Man page
normalize.scaling Man page
normvec Man page
normvec,PLMset-method Man page
nuse Man page
NUSE Man page
nuse,PLMset-method Man page
NUSE,PLMset-method Man page
pData<-,PLMset,data.frame-method Man page
pData,PLMset-method Man page
phenoData<-,PLMset,AnnotatedDataFrame-method Man page
phenoData,PLMset-method Man page
PLM.designmatrix Man page
PLM.designmatrix2 Man page
PLM.designmatrix3 Man page
PLMset Man page
PLMset2exprSet Man page
PLMset-class Man page
preprocess Man page
pset2eset Man page
pseudoColorBar Man page
pseudoPalette Man page
ReadRMAExpress Man page
resid Man page
resid<- Man page
resid<-,PLMset-method Man page
resid,PLMset-method Man page
residSE Man page
residSE,PLMset-method Man page
residuals Man page
residuals<- Man page
residuals<-,PLMset-method Man page
residuals,PLMset-method Man page
RLE Man page
RLE,PLMset-method Man page
rmaPLM Man page
sampleNames<- Man page
sampleNames<-,PLMset,character-method Man page
sampleNames,PLMset-method Man page
se Man page
se<- Man page
se.const Man page
se.const,PLMset-method Man page
se<-,PLMset-method Man page
se,PLMset-method Man page
se.probe Man page
se.probe,PLMset-method Man page
show,PLMset-method Man page
summary,PLMset-method Man page
threestep Man page
threestepPLM Man page
varcov Man page
varcov,PLMset-method Man page
verify.bg.param Man page
verify.constraint.types Man page
verify.model.param Man page
verify.norm.param Man page
verify.output.param Man page
verify.variable.types Man page
weights Man page
weights<- Man page
weights<-,PLMset-method Man page
weights,PLMset-method Man page

Files

affyPLM/CHANGELOG
affyPLM/DESCRIPTION
affyPLM/NAMESPACE
affyPLM/R
affyPLM/R/LESN.R affyPLM/R/PLMSet2exprSet.R affyPLM/R/PLMset.R affyPLM/R/ReadRMAExpress.R affyPLM/R/bg.correct.gcrma.R affyPLM/R/fitPLM.R affyPLM/R/init_fns.R affyPLM/R/internalfunctions.R affyPLM/R/normalize.exprSet.R affyPLM/R/normalize.scaling.R affyPLM/R/preprocess.R affyPLM/R/quantile_extensions.R affyPLM/R/rmaPLM.R affyPLM/R/threestep.R affyPLM/R/threestepPLM.R
affyPLM/build
affyPLM/build/vignette.rds
affyPLM/inst
affyPLM/inst/CITATION
affyPLM/inst/doc
affyPLM/inst/doc/AffyExtensions.R
affyPLM/inst/doc/AffyExtensions.Rnw
affyPLM/inst/doc/AffyExtensions.pdf
affyPLM/inst/doc/MAplots.R
affyPLM/inst/doc/MAplots.Rnw
affyPLM/inst/doc/MAplots.pdf
affyPLM/inst/doc/QualityAssess.R
affyPLM/inst/doc/QualityAssess.Rnw
affyPLM/inst/doc/QualityAssess.pdf
affyPLM/inst/doc/ThreeStep.R
affyPLM/inst/doc/ThreeStep.Rnw
affyPLM/inst/doc/ThreeStep.pdf
affyPLM/man
affyPLM/man/MAplot.Rd affyPLM/man/PLMset-class.Rd affyPLM/man/PLMset2exprSet.Rd affyPLM/man/ReadRMAExpress.Rd affyPLM/man/affyPLM-internal.Rd affyPLM/man/bg.correct.LESN.Rd affyPLM/man/fitPLM.Rd affyPLM/man/normalize.exprSet.Rd affyPLM/man/normalize.quantiles.probeset.Rd affyPLM/man/normalize.scaling.Rd affyPLM/man/preprocess.Rd affyPLM/man/pseudo.Rd affyPLM/man/rmaPLM.Rd affyPLM/man/threestep.Rd affyPLM/man/threestepPLM.Rd
affyPLM/src
affyPLM/src/LESN.c
affyPLM/src/LESN.h
affyPLM/src/Makevars
affyPLM/src/Makevars.win
affyPLM/src/PLM_avg_log.c
affyPLM/src/PLM_avg_log.h
affyPLM/src/PLM_biweight.c
affyPLM/src/PLM_biweight.h
affyPLM/src/PLM_log_avg.c
affyPLM/src/PLM_log_avg.h
affyPLM/src/PLM_medianPM.c
affyPLM/src/PLM_medianPM.h
affyPLM/src/PLM_median_logPM.c
affyPLM/src/PLM_median_logPM.h
affyPLM/src/PLM_medianpolish.c
affyPLM/src/PLM_medianpolish.h
affyPLM/src/PLM_modelmatrix.c
affyPLM/src/PLM_modelmatrix.h
affyPLM/src/SCAB.c
affyPLM/src/chipbackground.c
affyPLM/src/common_types.c
affyPLM/src/common_types.h
affyPLM/src/do_PLMrlm.c
affyPLM/src/do_PLMrlm.h
affyPLM/src/do_PLMrma.c
affyPLM/src/do_PLMrma.h
affyPLM/src/do_PLMthreestep.c
affyPLM/src/do_PLMthreestep.h
affyPLM/src/dqrls.h
affyPLM/src/idealmismatch.c
affyPLM/src/idealmismatch.h
affyPLM/src/lm_threestep.c
affyPLM/src/lm_threestep.h
affyPLM/src/matrix_functions.c
affyPLM/src/matrix_functions.h
affyPLM/src/nthLargestPM.c
affyPLM/src/nthLargestPM.h
affyPLM/src/preprocess.c
affyPLM/src/preprocess.h
affyPLM/src/psi_fns.c
affyPLM/src/psi_fns.h
affyPLM/src/qnorm_probeset.c
affyPLM/src/qnorm_probeset.h
affyPLM/src/read_rmaexpress.c
affyPLM/src/rlm_PLM.c
affyPLM/src/rlm_threestep.c
affyPLM/src/rlm_threestep.h
affyPLM/src/rmaPLM_pseudo.c
affyPLM/src/rmaPLM_pseudo.h
affyPLM/src/rma_PLM.c
affyPLM/src/rma_common.c
affyPLM/src/rma_common.h
affyPLM/src/scaling.c
affyPLM/src/scaling.h
affyPLM/src/threestep.c
affyPLM/src/threestep_PLM.c
affyPLM/src/threestep_common.c
affyPLM/src/threestep_common.h
affyPLM/src/threestep_summary.c
affyPLM/src/threestep_summary.h
affyPLM/src/threestep_summary_methods.c
affyPLM/src/threestep_summary_methods.h
affyPLM/src/threestep_summary_methods_param.h
affyPLM/src/transfns.c
affyPLM/src/transfns.h
affyPLM/tests
affyPLM/tests/C_code_tests.R
affyPLM/tests/PLM_tests.R
affyPLM/tests/preprocess_tests.R
affyPLM/tests/threestepPLM_tests.R
affyPLM/vignettes
affyPLM/vignettes/00Index.dcf
affyPLM/vignettes/AffyExtensions.Rnw
affyPLM/vignettes/AffyExtensions.bib
affyPLM/vignettes/MAplots.Rnw
affyPLM/vignettes/QualityAssess.Rnw
affyPLM/vignettes/ThreeStep.Rnw
affyPLM/vignettes/negresid.png
affyPLM/vignettes/posresid.png
affyPLM/vignettes/resid.png
affyPLM/vignettes/weights.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.