GitHub - SomaLogic/SomaLogic-Data: 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 their '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. (original) (raw)

SomaLogic-Data

The ADAT files included in this repository are 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. Data in this file is not intended for biological analysis purposes or to provide any metrics for SomaScan data in general.

Files

• example_data.adat
• example_data_v4.1_plasma.adat
• example_data_v5.0_plasma.adat

Installation

The example ADAT files in this repository can be retrieved in one of two ways:

1. Cloning the repository to your local machine
2. Using wget to retrieve individual ADAT files from the repository; see examples below

Retrieve just the 5k (v4.0) ADAT

wget https://github.com/SomaLogic/SomaLogic-Data/raw/main/example_data.adat

Retrieve just the 7k (v4.1) ADAT

wget https://github.com/SomaLogic/SomaLogic-Data/raw/main/example_data_v4.1_plasma.adat

Retrieve just the 11k (v5.0) ADAT

wget https://github.com/SomaLogic/SomaLogic-Data/raw/main/example_data_v5.0_plasma.adat

SomaScan Versions

ADAT File Format

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:

• 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 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 its left contains sample-specific (e.g. clinical) information.

Example File Description

The file, example_data.adat, contains a SomaScan V4.0 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 from four (4) 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)

The second file, example_data_v4.1_plasma.adat, contains a SomaScan v4.1 study from the same set of human samples. RFU measurements have been altered protect PII in this file as well. There are 163 EDTA Plasma samples from four (4) 96-well plate runs which include the following:

• 163 clinical samples
• 20 calibrators
• 12 QC samples
• 12 Buffer samples

The third file, example_data_v5.0_plasma.adat, contains a SomaScan v5.0 study from the same set of human samples. RFU measurements have been altered protect PII in this file as well. There are 163 EDTA Plasma samples from twelve (12) 96-well plate runs which include the following:

• 163 clinical samples
• 60 calibrators
• 36 QC samples
• 36 Buffer samples

Data Processing

The standard data normalization procedure for EDTA-plasma samples was applied to all three (3) datasets.

Sample and Analyte Annotations

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.

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:

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:

Parsers and Programatic Tools for ADAT Files

• R package: SomaDataIO
• Python module: Canopy
• Digital Tools: DataDelve Statistics

SomaLogic-Datawas developed by the Bioinformatics Dept. atSomaLogic Operating Co., Inc.