runQC {piano} | R Documentation

## 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 piano.rpkg@gmail.com and Intawat Nookaew piano.rpkg@gmail.com

### 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)

[Package piano version 2.2.0 Index]