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The Assay File provides references to assay results including measurements, images, raw data files, derived data files, image files, and other file types. There can be multiple Assay Files per study.
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TABLE 1: Example Subset of the Assay File Format
A | B | CD | E | |
|---|---|---|---|---|
Sample Name | Assay Name | Measurement Value[z-average(hydrodynamic diameter)] | Statistic | Unit |
NCL-20-Sample11 | size by DLS assay | 5.2 | z-average | nm |
NCL-20-Sample22 | size by DLS assay | 8.6z-average | nm |
Fields
According to the ISA-TAB specification, the Assay File has different types of fields called nodes, attributes of nodes, qualifiers of nodes’ attributes, and other valid fields. In support of ISA-TAB-Nano, extensions were applied to the Assay File to record the endpoint value of an assay measurement (Measurement Value) and to capture the statistical measures (Statistic) associated with a measurement or factor value.
The Assay File supports the following types of information:
- Source or sample Sample name
- Assay protocol reference and , protocol parameter valuesAssay name, performer, and date the assay protocol was performed
- Assay name
- Assay factor values including units and statistics, if applicable
- Assay measurement values including units and statisticsqualitifed by statistics, if applicable
- Raw Image files, raw data files, derived data files or image other files, if applicable
Nodes
Source Name---The unique identification name of the source referred to from within the study file. This column is used only if the source is the same as the sample in an assay. Source names can be qualified only using Comment.
Sample Name--- The unique identification name of the sample, which is referred to from within the study file. The sample is obtained after the application of a protocol. Sample names can be qualified only using Comment.
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Parameter Value [ ]--- Value of a parameter, which is kept constant, when applying a protocol. The parameter term is written within brackets and must match the term used as value for the study protocol parameter name in the investigation file.
Measurement Value [statistic(measurement name)]---The endpoint of the assay. This field is used Measurement value names are described in brackets or parenthesis if a statistics (e.g., mean, standard deviation) is applied to the measurement (Syntax: Measurement Value[statistic(<measurement name>)]). A statistic is only required for statistical measures. This concept is introduced in ISA-TAB-Nano to capture measurement outputs recorded in summary data.
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