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.
example_data.adatexample_data_v4.1_plasma.adatexample_data_v5.0_plasma.adatThe example ADAT files in this repository can be retrieved in one of two ways:
Cloning the repository to your local machine
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.adatcommercial name menu version size example file 5k V4 5284
example_data.adat 7k v4.1 7596 example_data_v4.1_plasma.adat 11k v5.0 11083 example_data_v5.0_plasma.adat
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.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:
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:
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:
The standard data normalization procedure for EDTA-plasma samples was applied to all three (3) datasets.
Sample and Analyte AnnotationsIn 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.
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:
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) 1.04Information 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:
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 Parsers and Programatic Tools for ADAT FilesSomaLogic-Data was developed by the Bioinformatics Dept. at SomaLogic Operating Co., Inc.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4