Using item properties as experimental factors - how could this be implemented?

[Johan Vallon-Christersson]

Would it be possible to somehow make item properties (or some selected item properties) available for use as experimental factors?

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Use case: An experiment include 20 rawbioassays, e.g., gene expression analysis of lung cancer biopsies. The raw bioassays are derived from 20 samples (the biopsies) annotated with a number of biologically and clinically relevant annotations, e.g., lung cancer type, tumor size, and so on. These annotations are used as experimental factors and the user can analyze differences in gene expression between the annotation type values.

However, the user is concerned that a number of technical parameters, not related to the biology of lung cancer, might be confounding factors and affect the analysis. For example, if insufficient care has been devoted to the experimental design, technical factors, such as scanner (the hardware used to scan array slides), might correlate with experimental factors derived from the samples, e.g., if two different scanners have been used. That is, a user might like to (or rather should always carefully) examine whether there is a correlation between gene expression and technical parameters such as scanner, array batch, hybridization date, protocols, and so on.

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Naturally, a user could export item properties, e.g., scanner, and then annotate the scans with scanner name using an annotation type. This is, however, not a particularly pretty solution as: the information is redundant (inputted twice), and there is no association between the property and the annotation type, i.e., if scan properties are changes the annotation values remain unaltered.

Some thoughts:

• Could a special form of annotation types be connected to item properties so that annotation values are derived from the item property value?
• Alternatively, could item properties be used directly as experimental factors?
• Is there already support for something similar?

It might be worthwhile to discuss this further and come up with a solution that enable users to analyze data in relation to item properties that may constitute confounding factors in experiments.

[Nicklas Nordborg]

This will not be possible in the current version. Might be considered for BASE 3.0.

[Johan Vallon-Christersson]

Just playing with thoughts of how the described user functionality could be made possible under BASE 2. For instance, is it not possible to implement a plugin that does the following?

• collects item properties
• updates annotations

The user could, e.g., in Scans list view, run such a plugin and specify:

• annotation type that should be used/updated, e.g., My_Scanner_Name.
• scans to annotate/update, e.g., selected, page, or all pages.
• item property to collect, e.g., Scanner

Such a plugin could have a user interface somewhat similar to the annotation importer plugin. Of course, this is sort or a tweak; redundant information will be stored and it's up to the user to make sure that information is updated if properties are changed.

[Nicklas Nordborg]

Yes that should be possible. It can sort of be done with the current batch importer+annotation importer already. Assuming that items are created with the batch importer and that this file contains relevant information about scanner, protocols, etc, the annotation importer can use the same columns from the same file to also import the annotations. It's about the same amount of work (manual clicking to set the importer options) as described in the previous post. If the items were not created with the batch importer the only extra step involved is to run the table exporter to create the file.