runQC: Run quality control

In varemo/piano: Platform for integrative analysis of omics data

Run quality control

Description

Performs a set of quality control methods and produces the results as figures.

Usage

runQC(
  arrayData,
  rnaDeg = TRUE,
  nuseRle = TRUE,
  hist = TRUE,
  boxplot = TRUE,
  pca = TRUE,
  colorFactor = 1,
  colors = c("red", "green", "blue", "yellow", "orange", "purple", "tan", "cyan",
    "gray60", "black", "white"),
  save = FALSE,
  verbose = TRUE
)

Arguments

arrayData	an object of class ArrayData.
rnaDeg	should RNA degradation be detected? Defaults to TRUE.
nuseRle	should Normalized Unscaled Standard Errors (NUSE) and Relative Log Expressions (RLE) be calculated? Defaults to TRUE.
hist	produce histograms of expression values? Defaults to TRUE.
boxplot	produce boxplots of expression values? Defaults to TRUE.
pca	should PCA be run? Defaults to TRUE.
colorFactor	a number specifying which column of the setup (given by the ArrayData object) should be used for coloring information for the PCA. Defaults to 1.
colors	a character vector of colors to be used in the PCA plot.
save	should the figures be saved? Defaults to FALSE.
verbose	verbose? Defaults to TRUE.

Details

This function is essentially a wrapper for various available quality control functions for AffyBatch objects and normalized microarray data. RNA degradation (rnaDeg=TRUE) and NUSE & RLE (nuseRle=TRUE) require raw data (a dataRaw element in the ArrayData object).

The PCA uses prcomp on centralized normalized data.

Typical usages are:

 # Run all quality controls:
runQC(arrayData) 

Value

Does not return any object.

Author(s)

Leif Varemo [e-mail] and Intawat Nookaew [e-mail]

References

Brettschneider J, Collin F, Bolstad BM, and Speed TP. Quality assessment for short oligonucleotide arrays. Technometrics. (2007) In press

See Also

piano, loadMAdata, diffExp, AffyRNAdeg, fitPLM, AffyBatch, prcomp

Examples

  # Get path to example data and setup files:
  dataPath <- system.file("extdata", package="piano")

  # Load normalized data:
  myArrayData <- loadMAdata(datadir=dataPath, dataNorm="norm_data.txt.gz", platform="yeast2")

  # Run PCA only:
  runQC(myArrayData,rnaDeg=FALSE, nuseRle=FALSE, hist=FALSE, boxplot=FALSE)

varemo/piano documentation built on Sept. 19, 2022, 12:01 p.m.