plot_lumi_QC_all: Perform all of the QC plots that are mentioned in the lumi...

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

Perform all of the QC plots that are mentioned in the lumi vignette. It creates a density plot, boxplot, PCA, HCL, CV-plot, pairs and MA plots. The pairs and MA plot can take a LONG time (>10mins?) if you have lots of arrays, so you can skip these plots using the MA=FALSE and pairs=FALSE arguments

Usage

  plot_lumi_QC_all(x, dir, prefix,
    title.prefix = "Unnormalised", MA = TRUE, pairs = TRUE)

Arguments

x	a LumiBatch object.
dir	the directory to create the plot files
prefix	prefix the plot filename prefix. eg “unnorm”, “qnorm”, “vst-transformed”
title.prefix	default=“Unnormalised”
MA	logical: create MA plots vs the average array?
pairs	logical: create a pairs plot? WARNING, this takes ages if you have lots of arrays.

Note

The CV plot some times fails, even if you don't have missing data in your LumiBatch. In this case, you'll get this Error:
Error in density.default(newX[, i], ...) : 'x' contains missing values

Author(s)

Mark Cowley, 2008-10-23

Examples

## Not run: 
dir.create("QC/01.unnorm")
plot_lumi_QC_all(x.raw, "QC/01.unnorm/", "raw", "Unnormalised")
dir.create("QC/02.transformed")
plot_lumi_QC_all(x.transformed, "QC/02.transformed/", "vst", "VST Transformed")
dir.create("QC/03.rsn")
plot_lumi_QC_all(x.norm.rsn, "QC/03.rsn/", "rsn", "RSN Normalised")

## End(Not run)

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.