# Methods for Spike-in Arrays

## Documentation for package ‘spkTools’ version 1.32.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

spkTools-package | Tools for Spike-in Data Analysis and Visualization
affy | SpikeInExpressionSet of Affymetrix Spike-in Experiment Data
class:SpikeInExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
initialize-method | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
plotSpkBox | Boxplots of Fold Changes Calculated by spkBox
spikeIn | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
spikeIn-method | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
spikeIn<--method | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
SpikeInExpressionSet | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
SpikeInExpressionSet-class | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
SpikeInExpressionSet-methods | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
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
spkSplit | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
spkSplit-method | Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
spkTools | Tools for Spike-in Data Analysis and Visualization
spkVar | Spike-in Variance
summarySpkBox | Summary of Fold Changes Calculated by spkBox