summarizeAtlasExperiment: Summarize an Expression Atlas experiment with Bioconductor...

In ebi-gene-expression-group/internal-ExpressionAtlas: Functions and Classes for EMBL-EBI Expression Atlas Data

Description

Create a SimpleList object containing ExpressionSet, SummarizedExperiment, and/or MAList objects storing data from an Expression Atlas experiment.

Usage

	summarizeAtlasExperiment( experimentAccession, atlasExperimentDirectory )

Arguments

experimentAccession	A character string containing the ArrayExpress accession of the experiment
atlasExperimentDirectory	Path to the directory containing the Atlas XML config file and expressions matrices. Optionally, a shell environment variable SDRF_PATH can be defined containing the path to the SDRF file.

Value

A SimpleList object representing one Expression Atlas experiment. Each element is either an ExpressionSet, SummarizedExperiment, or MAList object.

For microarray experiments, the elements are named according to their ArrayExpress array design accession. For RNA-seq experiments, there will only be one element, named "rnaseq".

SummarizedExperiment objects are used for RNA-seq data. They contain un-normalized, raw counts created with HTSeq. ExpressionSet objects are used for 1-colour microarray data. MAList objects are used for 2-colour microarray data. Microarray objects contain normalized intensity values. Affymetrix intensities are normalized using RMA, from the oligo package. Agilent 1-colour array intensities are normalized using between-array quantile normalization in the limma package. Agilent 2-colour array intensities are normalized using within-array loess normalization in limma.

Examples

## Not run: 
# Summarize an Atlas microarray experiment.
arrayExperimentSummaryList <- summarizeAtlasExperiment( 
	"E-MEXP-1025", 
	system.file( "extdata", "E-MEXP-1025", package = "ExpressionAtlasInternal" ) 
)

# Get some ExpressionSet objects.
expressionSet_affy18 <- arrayExperimentSummaryList[[ "A-AFFY-18" ]]
expressionSet_affy19 <- arrayExperimentSummaryList[[ "A-AFFY-19" ]]

# See the normalization method used.
preproc( experimentData( expressionSet_affy18 ) )

# Summarize an Atlas RNA-seq experiment.
rnaseqExperimentSummaryList <- summarizeAtlasExperiment(
	"E-GEOD-38400",
	system.file( "extdata", "E-GEOD-38400", package = "ExpressionAtlasInternal" )
)

# Get the SummarizedExperiment object.
summarizedExperiment <- rnaseqExperimentSummaryList$rnaseq

# Get the analysis methods.
analysisMethods <- exptData( summarizedExperiment )

# See what methods are documented.
names( analysisMethods )

# See the filtering steps used.
analysisMethods$filtering

## End(Not run)

ebi-gene-expression-group/internal-ExpressionAtlas documentation built on Aug. 7, 2021, 9:28 p.m.