affyPLM: Methods for fitting probe-level models
Version 1.52.1

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>
Bioconductor views Microarray OneChannel Preprocessing QualityControl
Date of publicationNone
MaintainerBen Bolstad <bmb@bmbolstad.com>
LicenseGPL (>= 2)
Version1.52.1
URL https://github.com/bmbolstad/affyPLM
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("affyPLM")

Popular man pages

affyPLM-internal: Internal affyPLM functions
normalize.exprSet: Normalization applied to ExpressionSets
normalize.scaling: Scaling normalization
PLMset2exprSet: Convert a PLMset to an ExpressionSet
PLMset-class: Class PLMset
ReadRMAExpress: Read RMAExpress computed expression values
rmaPLM: Fit a RMA to Affymetrix Genechip Data as a PLMset
See all...

All man pages Function index File listing

Man pages

affyPLM-internal: Internal affyPLM functions
bg.correct.LESN: LESN - Low End Signal is Noise Background corrections
fitPLM: Fit a Probe Level Model to Affymetrix Genechip Data.
MAplot: Relative M vs. A plots
normalize.exprSet: Normalization applied to ExpressionSets
normalize.quantiles.probeset: Quantile Normalization applied to probesets
normalize.scaling: Scaling normalization
PLMset2exprSet: Convert a PLMset to an ExpressionSet
PLMset-class: Class PLMset
preprocess: Background correct and Normalize
pseudo: Coloring pseudo chip images
ReadRMAExpress: Read RMAExpress computed expression values
rmaPLM: Fit a RMA to Affymetrix Genechip Data as a PLMset
threestep: Three Step expression measures
threestepPLM: Three Step expression measures returned as a PLMset

Functions

Files

CHANGELOG
DESCRIPTION
NAMESPACE
R
R/LESN.R
R/PLMSet2exprSet.R
R/PLMset.R
R/ReadRMAExpress.R
R/bg.correct.gcrma.R
R/fitPLM.R
R/init_fns.R
R/internalfunctions.R
R/normalize.exprSet.R
R/normalize.scaling.R
R/preprocess.R
R/quantile_extensions.R
R/rmaPLM.R
R/threestep.R
R/threestepPLM.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/AffyExtensions.R
inst/doc/AffyExtensions.Rnw
inst/doc/AffyExtensions.pdf
inst/doc/MAplots.R
inst/doc/MAplots.Rnw
inst/doc/MAplots.pdf
inst/doc/QualityAssess.R
inst/doc/QualityAssess.Rnw
inst/doc/QualityAssess.pdf
inst/doc/ThreeStep.R
inst/doc/ThreeStep.Rnw
inst/doc/ThreeStep.pdf
man
man/MAplot.Rd
man/PLMset-class.Rd
man/PLMset2exprSet.Rd
man/ReadRMAExpress.Rd
man/affyPLM-internal.Rd
man/bg.correct.LESN.Rd
man/fitPLM.Rd
man/normalize.exprSet.Rd
man/normalize.quantiles.probeset.Rd
man/normalize.scaling.Rd
man/preprocess.Rd
man/pseudo.Rd
man/rmaPLM.Rd
man/threestep.Rd
man/threestepPLM.Rd
src
src/LESN.c
src/LESN.h
src/Makevars
src/Makevars.win
src/PLM_avg_log.c
src/PLM_avg_log.h
src/PLM_biweight.c
src/PLM_biweight.h
src/PLM_log_avg.c
src/PLM_log_avg.h
src/PLM_medianPM.c
src/PLM_medianPM.h
src/PLM_median_logPM.c
src/PLM_median_logPM.h
src/PLM_medianpolish.c
src/PLM_medianpolish.h
src/PLM_modelmatrix.c
src/PLM_modelmatrix.h
src/SCAB.c
src/chipbackground.c
src/common_types.c
src/common_types.h
src/do_PLMrlm.c
src/do_PLMrlm.h
src/do_PLMrma.c
src/do_PLMrma.h
src/do_PLMthreestep.c
src/do_PLMthreestep.h
src/dqrls.h
src/idealmismatch.c
src/idealmismatch.h
src/lm_threestep.c
src/lm_threestep.h
src/matrix_functions.c
src/matrix_functions.h
src/nthLargestPM.c
src/nthLargestPM.h
src/preprocess.c
src/preprocess.h
src/psi_fns.c
src/psi_fns.h
src/qnorm_probeset.c
src/qnorm_probeset.h
src/read_rmaexpress.c
src/rlm_PLM.c
src/rlm_threestep.c
src/rlm_threestep.h
src/rmaPLM_pseudo.c
src/rmaPLM_pseudo.h
src/rma_PLM.c
src/rma_common.c
src/rma_common.h
src/scaling.c
src/scaling.h
src/threestep.c
src/threestep_PLM.c
src/threestep_common.c
src/threestep_common.h
src/threestep_summary.c
src/threestep_summary.h
src/threestep_summary_methods.c
src/threestep_summary_methods.h
src/threestep_summary_methods_param.h
src/transfns.c
src/transfns.h
tests
tests/C_code_tests.R
tests/PLM_tests.R
tests/preprocess_tests.R
tests/threestepPLM_tests.R
vignettes
vignettes/00Index.dcf
vignettes/AffyExtensions.Rnw
vignettes/AffyExtensions.bib
vignettes/MAplots.Rnw
vignettes/QualityAssess.Rnw
vignettes/ThreeStep.Rnw
vignettes/negresid.png
vignettes/posresid.png
vignettes/resid.png
vignettes/weights.png
affyPLM documentation built on May 20, 2017, 10:09 p.m.

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