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- New Analyte annotations and Row/sample data field descriptions were added to the README.md file - this relates to a question in the `SomaDataIO` package; issue SomaLogic/SomaDataIO#12 Co-authored-by: lcuddeback <[email protected]> Co-authored-by: Alex Poole <[email protected]>
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| # SomaLogic-Data | ||
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| ### File: example_data.adat | ||
| ## File: example_data.adat | ||
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| #### Overview | ||
| ### Overview | ||
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| The `example_data.adat` is intended to provide existing and prospective | ||
| SomaLogic customers an example data file to enable analysis preparation prior | ||
| to receipt of SomaScan data, and also for those generally curious about the | ||
| SomaScan data deliverable. It is **not** intended to be used as a control | ||
| group for studies or provide any metrics for SomaScan data in general. | ||
| SomaScan data deliverable. Data in this file is **not** intended for | ||
| biological analysis purposes or to provide any metrics for SomaScan data in | ||
| general. | ||
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| #### ADAT File Format | ||
| ### ADAT File Format | ||
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| The ADAT file format is a SomaLogic-specific, tab-delimited text file designed | ||
| to store SomaScan study data. This format is intended to be flexible and | ||
| self-describing. The fields in this example file may be different than the | ||
| fields in the \*.adat file for your study. However, all \*.adat files are comprised | ||
| of four main sections arranged in the following order: | ||
| fields in the \*.adat file for your study. However, all \*.adat files are | ||
| comprised of four main sections arranged in the following order: | ||
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| - `HEADER` - Study-level information about the SomaScan experiment and how the | ||
| data was processed. | ||
| - `COL_DATA` - Field names and type associated with the SOMAmer reagents | ||
| (columns). | ||
| - `ROW_DATA` - Field names and type associated with sample metadata (rows). | ||
| - `ROW_DATA` - Field names and type associated with sample information (rows). | ||
| - `TABLE_BEGIN` - This section contains the experimental data organized into a | ||
| data matrix of SOMAmer Reagents (columns) by samples (rows). SomaScan measurements | ||
| are in relative flourescent units (RFU). The data block directly above the | ||
| measurement matrix describes the SOMAmer reagents and the data block to | ||
| data matrix of SOMAmer Reagents (columns) by samples (rows). SomaScan | ||
| measurements are in relative flourescent units (RFU). The data block directly | ||
| above the measurement matrix describes the SOMAmer reagents and the data block | ||
| to its left contains sample-specific (e.g. clinical) information. | ||
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| #### Example File Description | ||
| ### Example File Description | ||
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| This file, `example_data.adat`, contains a SomaScan V4 study from healthy | ||
| normal individuals. The RFU measurements themselves and other identifiers | ||
| have been altered to protect personally identifiable information (PII), | ||
| but also retain underlying biological signal as much as possible. | ||
| There are 192 total EDTA-plasma samples across two 96-well plate runs | ||
| This file, `example_data.adat`, contains a SomaScan V4 study from a set of | ||
| human samples. The RFU measurements themselves and other identifiers | ||
| have been altered to protect personally identifiable information (PII), | ||
| but also retain underlying biological signal as much as possible. | ||
| There are 192 total EDTA-plasma samples across two 96-well plate runs | ||
| which are broken down by the following types: | ||
| * 170 clinical samples | ||
| * 10 calibrators (replicate controls for combining data across runs) | ||
| * 6 QC samples (replicate controls used to assess run quality) | ||
| * 6 Buffer samples (no protein controls) | ||
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| #### Data Processing | ||
| ### Data Processing | ||
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| The standard V4 data normalization procedure for EDTA-plasma samples was | ||
| applied to this dataset. | ||
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| #### Parsers and programatic tools for \*.adat files | ||
| ## Sample and Analyte Annotations | ||
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| In a standard SomaLogic ADAT, the section of information that | ||
| sits directly above the measurement data (RFU data matrix) is | ||
| the column meta data, which contains detailed information | ||
| and annotations about the analytes, `SeqIds`, and their targets. | ||
| See section below for further information about available | ||
| fields and their descriptions. | ||
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| ### Analyte Annotations: | ||
| Information describing the *analytes* is found to the above | ||
| the data matrix in a standard SomaLogic ADAT. This information may | ||
| consist of the any or all of the following: | ||
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| | __Field__ | __Description__ | __Example__ | | ||
| | :----------------- | :------------------------------------ | :------------- | | ||
| | SeqId | SomaLogic sequence identifier | 2182-54\_1 | | ||
| | SeqidVersion | Version of SOMAmer sequence | 2 | | ||
| | SomaId | Target identifier, of the form SLnnnnnn (8 characters in length) | SL000318 | | ||
| | TargetFullName | Target name curated for consistency with UniProt name | Complement C4b | | ||
| | Target | SomaLogic Target Name | C4b | | ||
| | UniProt | UniProt identifier(s) | P0C0L4 P0C0L5 | | ||
| | EntrezGeneID | Entrez Gene Identifier(s) | 720 721 | | ||
| | EntrezGeneSymbol | Entrez Gene Symbol names | C4A C4B | | ||
| | Organism | Protein Source Organism | Human | | ||
| | Units | Relative Fluorescence Units | RFU | | ||
| | Type | SOMAmer target type | Protein | | ||
| | Dilution | Dilution mix assignment | 0.01% | | ||
| | PlateScale\_Reference | PlateScale reference value | 1378.85 | | ||
| | CalReference | Calibration sample reference value | 1378.85 | | ||
| | medNormRef\_ReferenceRFU | Median normalization reference value | 490.342 | | ||
| | Cal\_V4\_\<YY\>\_\<SSS\>\_\<PPP\> | Calibration scale factor (for given Year\_Study\_Plate) | 0.64 | | ||
| | ColCheck | QC acceptance criteria across all plates/sets | PASS | | ||
| | QcReference\_\<LLLLL\> | QC sample reference value (for given QC lot) | PASS | | ||
| | CalQcRatio\_V4\_\<YY\>\_\<SSS\>\_\<PPP\> | Post calibration median QC ratio to reference (for given Year\_Study\_Plate) | 1.04 | | ||
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| #### Sample Annotations: | ||
| Information describing the *samples* is typically found to the left of | ||
| the data matrix in a standard SomaLogic ADAT. This information may | ||
| consist of clinical information provided by the client, or run-specific | ||
| diagnostic information included for assay quality control. Below are | ||
| some examples of what may be present in this section: | ||
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| | __Field__ | __Description__ | __Examples__ | | ||
| | :---------------- | :------------------------------------------------ | :------------- | | ||
| | PlateId | Plate identifier | V4-18-004\_001, V4-18-004\_002 | | ||
| | ScannerID | Scanner used to analyze slide | SG12064173, SG14374437 | | ||
| | PlatePosition | Location on 96 well plate (A1-H12) | A1, H12 | | ||
| | SlideId | Agilent slide barcode | 258495800001 | | ||
| | Subarray | Agilent subarray (1 – 8) | 1,8 | | ||
| | SampleId | 1st form is Subject Identifier, 2nd form (calibrators, buffers) | 2031 | | ||
| | SampleType | 1st form for clinical samples (Sample), 2nd form as above | Sample, QC, Calibrator, Buffer | | ||
| | PercentDilution | Highest concentration the SOMAmer dilution groups | 20 | | ||
| | SampleMatrix | Sample matrix | Plasma-PPT | | ||
| | Barcode | 1D Barcode of aliquot | S622225 | | ||
| | Barcode2d | 2D Barcode of aliquot | 9876543210 | | ||
| | SampleNotes | Assay team sample observation | Cloudy, Low sample volume, Reddish | | ||
| | SampleDescription | Supplemental sample information | Plasma QC 1 | | ||
| | AssayNotes | Assay team run observation | Beads aspirated, Leak/Hole, Smear | | ||
| | TimePoint | Sample time point | Baseline | | ||
| | ExtIdentifier | Primary key for Subarray | EXID40000000032037 | | ||
| | SsfExtId | Primary key for sample | EID102733 | | ||
| | SampleGroup | Sample group | A, B | | ||
| | SiteId | Collection site | SomaLogic | | ||
| | TubeUniqueID | Unique tube identifier | 2031 | | ||
| | CLI | Cohort definition identifier | CLI6006F001 | | ||
| | HybControlNormScale | Hybridization control scale factor | 0.948304 | | ||
| | RowCheck | Normalization acceptance criteria for all row scale factors | PASS, FLAG | | ||
| | NormScale\_0\_5 | Median signal normalization scale factor (0.5% mix) | 1.02718 | | ||
| | NormScale\_0\_005 | Median signal normalization scale factor (0.005% mix) | 1.119754 | | ||
| | NormScale\_20 | Median signal normalization scale factor (20% mix) | 0.996148 | | ||
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| ## Parsers and Programatic Tools for \*.adat Files | ||
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| - R packge: [SomaDataIO](https://github.com/SomaLogic/SomaDataIO) | ||
| - Python module: [canopy.py](https://github.com/SomaLogic/Canopy) |