drLumi: Multiplex Immunoassays Data Analysis

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Contains quality control routines for multiplex immunoassay data, including several approaches for: treating the background noise of the assay, fitting the dose-response curves and estimating the limits of quantification.

Author
Hector Sanz [aut, cre], John Aponte [aut], Jaroslaw Harezlak [aut], Yan Dong [aut], Magdalena Murawska [aut], Clarissa Valim [aut], Aintzane Ayestaran [ctb], Ruth Aguilar [ctb], Gemma Moncunill [ctb]
Date of publication
2015-09-24 01:27:27
Maintainer
Hector Sanz <hector.sanz@isglobal.org>
License
GPL (>= 2)
Version
0.1.2

View on CRAN

Man pages

conf_bands
Confidence interval for a scluminex object
data_selection
Extracts samples information from a lum_export object or...
ecdata
Expected concentration data
est_conc
Estimates concentration given an scluminex object
get_outliers
Extract outliers from a scluminex object
intra_icc
Estimate ICC of a data.frame
invest
Estimate the concentration given a response value
loq_cv
Limits of quantifications estimation using coefficient of...
loq_derivatives
Limits of quantifications estimation using derivatives
loq_interval
Limits of quantifications estimation using interval method
lum_export
Extract and generates data.frame from lum_import object
lum_import
Import Luminex data
mfidata
Median Fluorescence Intensity data
plot.scluminex
Plot method for the scluminex class
scluminex
Estimates different models for each analyte.
SSexp
Self-Starting Nls exponential regression model
SSexpcons
Self-Starting Nls exponential constraint regression model
SSl4
Self-Starting Nls 4 parameters logistic regression model
SSl4cons
Self-Starting Nls 4 parameters logistic constraint regression...
SSl5
Self-Starting Nls 5 parameters logistic regression model
SSl5cons
Self-Starting Nls 5 parameters logistic constraint regression...
summary.scluminex
Summary of a scluminex object

Files in this package

drLumi
drLumi/inst
drLumi/inst/tests
drLumi/inst/tests/report_interval_loq.R
drLumi/inst/tests/test-data_selection.R
drLumi/inst/tests/invest_decreasing.R
drLumi/inst/tests/test-loq_interval.R
drLumi/inst/NEWS
drLumi/inst/extdata
drLumi/inst/extdata/plate1.csv
drLumi/inst/extdata/bead_data.zip
drLumi/inst/extdata/bead_data
drLumi/inst/extdata/bead_data/plate_P1_A2.csv
drLumi/inst/extdata/bead_data/plate_P1_A1.csv
drLumi/inst/extdata/toydata.R
drLumi/inst/doc
drLumi/inst/doc/drLumi.R
drLumi/inst/doc/drLumi.rnw
drLumi/inst/doc/drLumi.pdf
drLumi/tests
drLumi/tests/test-all.R
drLumi/NAMESPACE
drLumi/data
drLumi/data/ecdata.rda
drLumi/data/mfidata.rda
drLumi/R
drLumi/R/lum_import_fluor.R
drLumi/R/get_aic.R
drLumi/R/avgimport.R
drLumi/R/getPredict.R
drLumi/R/invest.R
drLumi/R/get_modelfit.R
drLumi/R/get_fitted.R
drLumi/R/plot.scluminex.R
drLumi/R/scluminex.R
drLumi/R/print.summary.scluminex.R
drLumi/R/define_data.R
drLumi/R/as.data.frame.summary.scluminex.R
drLumi/R/data_selection.R
drLumi/R/print.lum_export.R
drLumi/R/invest.loq.interval.R
drLumi/R/get_convergence.R
drLumi/R/intra_icc.R
drLumi/R/lum_import.default.R
drLumi/R/summary.scluminex.R
drLumi/R/mfidata.R
drLumi/R/geom_mean.R
drLumi/R/luminexData-internal.R
drLumi/R/lum_import.R
drLumi/R/est_conc.R
drLumi/R/plotLum.R
drLumi/R/derivative.R
drLumi/R/get_neilltest.R
drLumi/R/sampleimport.R
drLumi/R/extractcoef.R
drLumi/R/regionimport.R
drLumi/R/print.scluminex.R
drLumi/R/fix_name.R
drLumi/R/invest.fun.R
drLumi/R/conf_bands.R
drLumi/R/get_outliers.R
drLumi/R/summary.loq.R
drLumi/R/loq_interval.R
drLumi/R/print.loq.R
drLumi/R/scurveimport.R
drLumi/R/loq_derivatives.R
drLumi/R/lum_import_bead.R
drLumi/R/SSFunctions.R
drLumi/R/batchimport.R
drLumi/R/convert_time.R
drLumi/R/bead_fun.R
drLumi/R/get_rsq.R
drLumi/R/compair.R
drLumi/R/wellsimport.R
drLumi/R/plotRes.R
drLumi/R/ecdata.R
drLumi/R/print.lum_import.R
drLumi/R/plotQQnorm.R
drLumi/R/as.data.frame.scluminex.R
drLumi/R/loq_cv.R
drLumi/R/lum_export.R
drLumi/vignettes
drLumi/vignettes/unnamed-chunk-35.pdf
drLumi/vignettes/flow.pdf
drLumi/vignettes/drLumi_vignette.bib
drLumi/vignettes/unnamed-chunk-19.pdf
drLumi/vignettes/unnamed-chunk-26-1.pdf
drLumi/vignettes/unnamed-chunk-34.pdf
drLumi/vignettes/qqplot.pdf
drLumi/vignettes/unnamed-chunk-36.pdf
drLumi/vignettes/loqder.pdf
drLumi/vignettes/unnamed-chunk-5.tex
drLumi/vignettes/unnamed-chunk-57-1.pdf
drLumi/vignettes/drLumi.rnw
drLumi/vignettes/resplot.pdf
drLumi/vignettes/unnamed-chunk-54-1.pdf
drLumi/vignettes/unnamed-chunk-38.pdf
drLumi/vignettes/unnamed-chunk-14.pdf
drLumi/vignettes/unnamed-chunk-37.pdf
drLumi/vignettes/unnamed-chunk-52-1.pdf
drLumi/vignettes/unnamed-chunk-13.pdf
drLumi/vignettes/comparisonbackground.pdf
drLumi/vignettes/flow.tex
drLumi/vignettes/scurveplot.pdf
drLumi/vignettes/unnamed-chunk-12.pdf
drLumi/vignettes/backcomparison.pdf
drLumi/vignettes/flow.synctex.gz
drLumi/vignettes/test.vrb
drLumi/vignettes/unnamed-chunk-18.pdf
drLumi/vignettes/unnamed-chunk-33.pdf
drLumi/vignettes/framed.sty
drLumi/MD5
drLumi/build
drLumi/build/vignette.rds
drLumi/DESCRIPTION
drLumi/man
drLumi/man/est_conc.Rd
drLumi/man/mfidata.Rd
drLumi/man/plot.scluminex.Rd
drLumi/man/invest.Rd
drLumi/man/SSl5cons.Rd
drLumi/man/ecdata.Rd
drLumi/man/data_selection.Rd
drLumi/man/lum_export.Rd
drLumi/man/SSl4.Rd
drLumi/man/loq_derivatives.Rd
drLumi/man/get_outliers.Rd
drLumi/man/conf_bands.Rd
drLumi/man/SSexp.Rd
drLumi/man/loq_interval.Rd
drLumi/man/lum_import.Rd
drLumi/man/SSl4cons.Rd
drLumi/man/scluminex.Rd
drLumi/man/SSexpcons.Rd
drLumi/man/SSl5.Rd
drLumi/man/summary.scluminex.Rd
drLumi/man/loq_cv.Rd
drLumi/man/intra_icc.Rd