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Mage FAQ

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About this FAQ

What is this FAQ?

It is the list of Frequently Asked Questions about the Chado Mage module.

How is it maintained?

It is now maintained as a Wiki on this site. You can help maintain it by adding questions and answers.

Is there other documentation?

See the Mage module documentation.

Using Mage

What happened to the Rad module?

It has been renamed Mage, this module.

What should be done with experiments with multiple arrays per sample?

Examples: genome tiling experiments, or multiple samples per array (Agilent and Illumina arrays).
There is a many-to-many between samples and hybridizations using the assay_biomaterial table. You assign your sample channel using the assay_biomaterial.channel attribute for a multi-channel array. Each tiling array hybridization in a tiling set would be considered a separate assay, and each would have a different assay.arraydesign_id.

How do you store files containing raw data?

Use acquisition.uri to point to the file outside the database, in the file system.

How can one trace the biomaterials back to get a sense of the level of technical and/or biological replication?

Use the experiment, factor, and treatment tables.

How do you create a reference from the results of a microarray experiment to the source of the data stored in the pub table?