microarray2dataset


The species corresponding to an probeset identifier can often be identified
from the prefix of the identifier (e.g. Bt.457.1.S1_at corresponds to
<em>Bos taurus</em> which is only associated with a single microarray platform
in the Ensembl BioMart). This table maps some manually curated unique patterns
to the corresponding species and microarray platform.


datasets

GOexpress

The package contains methods to visualise the expression profile
of genes from a microarray or RNA-seq experiment, and offers a
supervised clustering approach to identify GO terms containing genes
with expression levels that best classify two or more predefined groups of
samples. Annotations for the genes present in the expression dataset may
be obtained from Ensembl through the biomaRt package, if not provided by
the user. The default random forest framework is used to evaluate the
capacity of each gene to cluster samples according to the
factor of interest. Finally, GO terms are scored by averaging the
rank (alternatively, score) of their respective gene sets to cluster
the samples. P-values may be computed to assess the significance of GO
term ranking. Visualisation function include gene expression profile,
gene ontology-based heatmaps, and hierarchical clustering of
experimental samples using gene expression data.

Kevin Rue-Albrecht

Visualise microarray and RNAseq data using gene ontology annotations

microarray2dataset function

The <code>microarray2dataset.build</code> method stored in the <code>toolkit.R</code>
script was used to query the Ensembl BioMart server and build this table.

microarray2dataset: Table mapping probeset identifier prefixes to datasets in the Ensembl BioMart.

Description

Usage

Arguments

Value

Source

Details

Examples