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

In kevinrue/GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description

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 Bos taurus 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.

Usage

data(microarray2dataset)

Details

All Agilent microarray share the same prefix pattern, making it very difficult to differentiate. Many Affymetrix microarrays also share the same prefix "AFFX" for several probesets.

The dataset and microarray arguments of the GO_analyse method are the best way to specify which BioMart information should be used to annotate the features in your expression dataset.

Value

A data frame with 158 rows and the 6 columns. Rows are sorted alphabetically by species name and each refer to a unique combination of dataset and microarray identifier in the Ensembl BioMart. The columns are described below:

• dataset contains species-specific biomaRt dataset names.

• microarray contains the microarray identifier in the Ensembl BioMart dataset above.

• sample contains a sample probeset from this combination of Ensembl BioMart dataset and microarray.

• species contains an example probeset sampled from the corresponding Ensembl BioMart dataset and microarray.

• pattern contains the corresponding manually curated pattern representative of probesets for this microarray platform. This pattern may or may not be unique to the microarray. Therefore we encourage users to use the 'microarray' argument of the GO_analyse method to specify the Ensembl BioMart dataset to use.

• unique contains a boolean value stating whether the pattern was found unique to the microarray or not.

Source

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

Examples

data(microarray2dataset)
microarray2dataset

kevinrue/GOexpress documentation built on May 19, 2020, 7:23 p.m.