TRA: Technical replicate agreement (TRA) plot

In Mengbo-Li/ruvms: Removing Unwanted Variations in Mass-Spectrometry Data.

Technical replicate agreement (TRA) plot

Description

Technical replicate agreement (TRA) plots provide a visualisation diagnostic that measures the closeness among technical replicates.

Usage

TRA(
  data,
  replicates = NULL,
  M = NULL,
  col = NULL,
  ylim = NULL,
  printLabel = TRUE,
  printLegend = FALSE,
  guides = NULL,
  title = NULL
)

Arguments

data	The m-by-n data matrix with samples on the rows and measurements ( proteins etc.) on the columns. Missing data (NAs) are allowed.
replicates	A vector indicating which samples are replicates of each other. Obsolete when M is not NULL.
M	The replication structure matrix.
col	Color of the TRA boxes. Default is NULL.
ylim	The y-axis limits of the output plot.
printLabel	Logical. Whether to print the names of the technical replicates.
printLegend	Logical. Whether to print the color legend.
guides	Numeric. Horizontal dashed lines for reference.
title	Character. Title of the output plot.

Details

The assumption of TRA plots is that if all unwanted variations are effectively removed, replications of a unique effective sample are identical after normalisation, even if we do not declare them as replicates of each other

Value

The TRA plot.

References

Molania, R., Gagnon-Bartsch, J. A., Dobrovic, A., & Speed, T. P. (2019). A new normalization for Nanostring nCounter gene expression data. Nucleic acids research, 47(12), 6073-6083.

Mengbo-Li/ruvms documentation built on Nov. 14, 2023, 2:11 a.m.