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

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

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