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Description
1.1.1 Assay File
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---The assay file provides references to assay results including measurements, raw data files, derived data files, image files, and other file types. There can be multiple assay files per study.
File Format
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\---The nano-TAB assay file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers and row values. An example subset of this format is provided in TABLE 5. Please note, concepts specified within the bracket “\[ \]” are variables depending on the type of assay. |
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Fields
Nano-TAB Extensions---In support of nano-TAB, the extensions and constraints in Table 6 were applied to the ISA-TAB assay file and are further described in Section 5.6. One important extension is that nano-TAB allows the entry of summary data in the assay files through an optional field called Measurement Value, as described in TABLE 6.
1.1 Assay File1.1 .1 The assay file is a horizontally oriented spreadsheet, where the field names are organized as column headers in the first row. TABLE 23, TABLE 24, and TABLE 25, show an example of an assay file. 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. The assay file supports the following types of information:
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1.1.2.2.2 _Characteristic\[\]_\---An attribute for _sample name_ if the same attribute is not given in the study file. |
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1.1.2.3.4 _Parameter value\[<parameter term\]_\--\- 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. |
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1.1.2.4.1 _Unit_\---The standard of measurement used if the values for _characteristic_\[\], _parameter value\[\]_ or _factor value\[\]_ columns are quantitative and dimensional. If the term for _unit_ is taken from an ontology/controlled vocabulary, then its _term accession number_ and the _term source REF_ should be defined in the nano-TAB investigation file. |
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1.1.2.4.2 _Term Accession Number_\---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value in _source name_, _material type,_ _characteristic \[\]_, _parameter value\[\]_, _unit_ or _factor value\[\]_ columns. |
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1.1.2.5.1 _Factor Value\[<factor name>\]_\---The value of an independent variable manipulated by the experimentalist with the intention to affect the subject of study (i.e. stressor). Factor terms are given in brackets, and must be defined in the nano-TAB investigation file in the STUDY FACTORS section. Factor Value\[\] in assay file should reference technical variations (such as software, instrument or protocol variations). |
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1.1.2.5.2 _Comment\[\]_\---Any comment that provides additional information, which is added only when no other appropriate field exists. |
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