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Add 11k-v5.0 example data and update README (#6)
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- closes #6
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stufield committed Apr 9, 2024
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38 changes: 28 additions & 10 deletions README.md
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Expand Up @@ -12,10 +12,11 @@ purposes or to provide any metrics for SomaScan data in general.
---------------------


## Files
## Files

* `example_data.adat`
* `example_data_v4.1_plasma.adat`
* `example_data_v5.0_plasma.adat`


## Installation
Expand All @@ -33,6 +34,9 @@ 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
```


Expand All @@ -42,7 +46,7 @@ wget https://github.com/SomaLogic/SomaLogic-Data/raw/main/example_data_v4.1_plas
| --------------- | ------------ | ----- | -------------------------------- |
| 5k | V4 | 5284 | `example_data.adat` |
| 7k | v4.1 | 7596 | `example_data_v4.1_plasma.adat` |
| 11k | v5.0 | 11083 | `NA` |
| 11k | v5.0 | 11083 | `example_data_v5.0_plasma.adat` |


## ADAT File Format
Expand Down Expand Up @@ -85,14 +89,24 @@ There are 163 EDTA Plasma samples from four 96-well plate runs which
include the following:
* 163 clinical samples
* 20 calibrators
* 12 QC samples
* 12 Buffer samples
* 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 four 96-well plate runs which
include the following:
* 163 clinical samples
* 60 calibrators
* 36 QC samples
* 36 Buffer samples


## Data Processing

The standard V4 data normalization procedure for EDTA-plasma samples was
applied to this dataset.
The standard data normalization procedure for EDTA-plasma samples was
applied to all three (3) datasets.


## Sample and Analyte Annotations
Expand All @@ -104,7 +118,9 @@ and annotations about the analytes, `SeqIds`, and their targets.
See section below for further information about available
fields and their descriptions.

### Analyte Annotations:

### 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:
Expand All @@ -131,7 +147,9 @@ consist of the any or all of the following:
| 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 |

### Sample Annotations:

### 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
Expand Down Expand Up @@ -179,6 +197,6 @@ some examples of what may be present in this section:

---------------

[SomaLogic-Data](https://github.com/SomaLogic/SomaLogic-Data/)
was developed by the Bioinformatics Dept. at
[SomaLogic-Data](https://github.com/SomaLogic/SomaLogic-Data/)
was developed by the Bioinformatics Dept. at
[SomaLogic Operating Co., Inc.](http://www.somalogic.com)
470 changes: 470 additions & 0 deletions example_data_v5.0_plasma.adat

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