Package: spkTools 1.63.0

Matthew N McCall

spkTools: Methods for Spike-in Arrays

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

Authors:Matthew N McCall <[email protected]>, Rafael A Irizarry <[email protected]>

# Install 'spkTools' in R:

install.packages('spkTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On BioConductor:spkTools-1.63.0(bioc 3.21)spkTools-1.62.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated 5 months agofrom:c8630a9695. Checks:1 OK, 7 NOTE. Indexed: yes.

Last update: 2013-11-01
Started: 2013-11-01

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