boxplotAll_oligo: BoxPlots for quality control

In machalen/QualityGraphsOligo: Make quality graphs for microarray data based on objects obtained with oligo normalization.

Description

Function to make all boxplots required for quality control.

Usage

boxplotAll_oligo(ds, est_noctrls = NULL, Pset = NULL, picname, labels = NULL, conditions = NULL, colors = NULL, raw.bp = TRUE, RMA.bp = TRUE, RLE = TRUE, NUSE = TRUE, resDir = NULL)

Arguments

ds	GeneFeatureSet object obtained with: RawData <- read.celfiles(celFiles.s, sampleNames= celnames.s)
est_noctrls	Normalized expression matrix.
Pset	PLM object obtained from fitProbeLevelModel: Pset <- fitProbeLevelModel(RawData)
picname	Character with the output file name.
labels	Optional. Vector with sample names. Samples are in the same order as in the ds object. Default get sample names from the ds object.
conditions	Optional, vector with sample condition in the same order as samples appear in the ds object.
colors	Optional, vector with the colours corresponding to each condition.
raw.bp	Plot boxplots with raw data at log2 scale. Default TRUE.
RMA.bp	Plot boxplots with normalized log2 data. Default TRUE.
RLE	Plot boxplots with relative log expression values (RLE). Default TRUE.
NUSE	Plot boxplots with normalized unscaled standard errors (NUSE). Default TRUE.
resDir	Output results directory. Default is ResultsDir.

Details

This function outputs boxplots for quality assessment in microarray data using objects obtained with oligo package pre-processing. A boxplot with raw data, and a boxplot with Normalized data. Additionally reports relative log expression values (RLE), and normalized unscaled standard errors (NUSE).

Value

This function outputs plots in .png format in the resDir directory.

Author(s)

Magdalena Arnal Segura <[e-mail]>

machalen/QualityGraphsOligo documentation built on May 28, 2019, 2:32 a.m.