affyPLM: Methods for fitting probe-level models

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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.

Author
Ben Bolstad <bmb@bmbolstad.com>
Date of publication
None
Maintainer
Ben Bolstad <bmb@bmbolstad.com>
License
GPL (>= 2)
Version
1.50.0
URLs

View on Bioconductor

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

Files in this package

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