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spkTools (version 1.28.0)

Methods for Spike-in Arrays

Description

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

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Version

Version

1.28.0

License

GPL (>= 2)

Maintainer

Matthew N McCall

Last Published

February 15th, 2017

Functions in spkTools (1.28.0)

spkBox

Fold Change Calculations
spkAll

Spike-in Functions Wrapper
spkVar

Spike-in Variance
spkMA

MA Plots
spkBal

Quantify Microarry Spike-in Design Imbalance
spkDensity

Spike-in Density Plot
spkPairNS

Pairwise Comparisons for Non-Spike-in Genes
spkPot

Probability of being in the Top
affy

SpikeInExpressionSet of Affymetrix Spike-in Experiment Data
spkPair

Pairwise Comparisons for Spike-in Genes
spkAccSD

Accuracy Standard Deviation
plotSpkBox

Boxplots of Fold Changes Calculated by spkBox
spkQuantile

Empirical Quantiles
summarySpkBox

Summary of Fold Changes Calculated by spkBox
spkAnova

Anova Model for Microarray Spike-in Data
spkGNN

Genes Needed to Detect N True Positives
spkTools

Tools for Spike-in Data Analysis and Visualization
SpikeInExpressionSet-class

Class to Contain and Describe High-Throughput Expression Level Assays with Spike-in Data
spkSlope

Signal Detect Slope Plot