spkTools: Methods for Spike-in Arrays

The package contains functions that can be used to compare expression measures on different array platforms.

Author
Matthew N McCall <mccallm@gmail.com>, Rafael A Irizarry <rafa@jhu.edu>
Date of publication
None
Maintainer
Matthew N McCall <mccallm@gmail.com>
License
GPL (>= 2)
Version
1.30.0
URLs

View on Bioconductor

Man pages

affy
SpikeInExpressionSet of Affymetrix Spike-in Experiment Data
plotSpkBox
Boxplots of Fold Changes Calculated by spkBox
SpikeInExpressSet-class
Class to Contain and Describe High-Throughput Expression...
spkAccSD
Accuracy Standard Deviation
spkAll
Spike-in Functions Wrapper
spkAnova
Anova Model for Microarray Spike-in Data
spkBal
Quantify Microarry Spike-in Design Imbalance
spkBox
Fold Change Calculations
spkDensity
Spike-in Density Plot
spkGNN
Genes Needed to Detect N True Positives
spkMA
MA Plots
spkPair
Pairwise Comparisons for Spike-in Genes
spkPairNS
Pairwise Comparisons for Non-Spike-in Genes
spkPot
Probability of being in the Top
spkQuantile
Empirical Quantiles
spkSlope
Signal Detect Slope Plot
spkTools
Tools for Spike-in Data Analysis and Visualization
spkVar
Spike-in Variance
summarySpkBox
Summary of Fold Changes Calculated by spkBox

Files in this package

spkTools/DESCRIPTION
spkTools/NAMESPACE
spkTools/R
spkTools/R/AllClasses.R
spkTools/R/AllGenerics.R
spkTools/R/SpikeInExpressionSet-methods.R
spkTools/R/plotSpkBox.R
spkTools/R/spkAccSD.R
spkTools/R/spkAll.R
spkTools/R/spkAnova.R
spkTools/R/spkBal.R
spkTools/R/spkBox.R
spkTools/R/spkDensity.R
spkTools/R/spkGNN.R
spkTools/R/spkMA.R
spkTools/R/spkPair.R
spkTools/R/spkPairNS.R
spkTools/R/spkPot.R
spkTools/R/spkQuantile.R
spkTools/R/spkSlope.R
spkTools/R/spkVar.R
spkTools/R/summarySpkBox.R
spkTools/build
spkTools/build/vignette.rds
spkTools/data
spkTools/data/affy.rda
spkTools/inst
spkTools/inst/doc
spkTools/inst/doc/spkDoc.R
spkTools/inst/doc/spkDoc.Rnw
spkTools/inst/doc/spkDoc.pdf
spkTools/man
spkTools/man/SpikeInExpressSet-class.Rd
spkTools/man/affy.Rd
spkTools/man/plotSpkBox.Rd
spkTools/man/spkAccSD.Rd
spkTools/man/spkAll.Rd
spkTools/man/spkAnova.Rd
spkTools/man/spkBal.Rd
spkTools/man/spkBox.Rd
spkTools/man/spkDensity.Rd
spkTools/man/spkGNN.Rd
spkTools/man/spkMA.Rd
spkTools/man/spkPair.Rd
spkTools/man/spkPairNS.Rd
spkTools/man/spkPot.Rd
spkTools/man/spkQuantile.Rd
spkTools/man/spkSlope.Rd
spkTools/man/spkTools.Rd
spkTools/man/spkVar.Rd
spkTools/man/summarySpkBox.Rd
spkTools/vignettes
spkTools/vignettes/spkDoc.Rnw
spkTools/vignettes/spkDoc.bib