In a standard SomaLogic ADAT, the section of information that
sits directly above the measurement data (RFU data matrix) is
the column meta data (Col.Meta), which contains detailed information
and annotations about the analytes, SeqId()s, and their targets.
See section below for further information about available
fields and their descriptions. Use getAnalyteInfo() to
obtain an object containing this information for programmatic analyses,
and use getMeta() to obtain the column names representing the
row-specific meta data about the samples (see section below).
Col Meta (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:
| 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 |
Row Meta (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:
| 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 | 2.58E+11 |
| 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 | 1.91E+08 |
| 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, Covance |
| TubeUniqueID | Unique tube identifier | 1.12E+11 |
| 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 |
Examples
# Annotations/Col.Meta
tbl <- getAnalyteInfo(example_data)
tbl
#> # A tibble: 5,284 × 22
#> AptName SeqId SeqIdVersion SomaId TargetFullName Target UniProt
#> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 seq.10000.28 10000-… 3 SL019… Beta-crystall… CRBB2 P43320
#> 2 seq.10001.7 10001-7 3 SL002… RAF proto-onc… c-Raf P04049
#> 3 seq.10003.15 10003-… 3 SL019… Zinc finger p… ZNF41 P51814
#> 4 seq.10006.25 10006-… 3 SL019… ETS domain-co… ELK1 P19419
#> 5 seq.10008.43 10008-… 3 SL019… Guanylyl cycl… GUC1A P43080
#> 6 seq.10011.65 10011-… 3 SL019… Inositol poly… OCRL Q01968
#> 7 seq.10012.5 10012-5 3 SL014… SAM pointed d… SPDEF O95238
#> 8 seq.10013.34 10013-… 3 SL025… Fc_MOUSE Fc_MO… Q99LC4
#> 9 seq.10014.31 10014-… 3 SL007… Zinc finger p… SLUG O43623
#> 10 seq.10015.119 10015-… 3 SL014… Voltage-gated… KCAB2 Q13303
#> # ℹ 5,274 more rows
#> # ℹ 15 more variables: EntrezGeneID <chr>, EntrezGeneSymbol <chr>,
#> # Organism <chr>, Units <chr>, Type <chr>, Dilution <chr>,
#> # PlateScale_Reference <dbl>, CalReference <dbl>,
#> # Cal_Example_Adat_Set001 <dbl>, ColCheck <chr>,
#> # CalQcRatio_Example_Adat_Set001_170255 <dbl>,
#> # QcReference_170255 <dbl>, Cal_Example_Adat_Set002 <dbl>, …
# Row/sample Meta
r_m <- getMeta(example_data)
head(r_m)
#> [1] "PlateId" "PlateRunDate" "ScannerID" "PlatePosition"
#> [5] "SlideId" "Subarray"
# Normalization Scale Factors
grep("NormScale", r_m, value = TRUE)
#> [1] "HybControlNormScale" "NormScale_20" "NormScale_0_005"
#> [4] "NormScale_0_5"
# adat subset
example_data[1:3, head(r_m)]
#> ══ SomaScan Data ═════════════════════════════════════════════════════════
#> SomaScan version V4 (5k)
#> Signal Space 5k
#> Attributes intact ✓
#> Rows 3
#> Columns 6
#> Clinical Data 6
#> Features 0
#> ── Column Meta ───────────────────────────────────────────────────────────
#> ℹ SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt,
#> ℹ EntrezGeneID, EntrezGeneSymbol, Organism, Units, Type,
#> ℹ Dilution, PlateScale_Reference, CalReference,
#> ℹ Cal_Example_Adat_Set001, ColCheck,
#> ℹ CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,
#> ℹ Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255,
#> ℹ Dilution2
#> ── Tibble ────────────────────────────────────────────────────────────────
#> # A tibble: 3 × 7
#> row_names PlateId PlateRunDate ScannerID PlatePosition SlideId Subarray
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 258495800… Exampl… 2020-06-18 SG152144… H9 2.58e11 3
#> 2 258495800… Exampl… 2020-06-18 SG152144… H8 2.58e11 7
#> 3 258495800… Exampl… 2020-06-18 SG152144… H7 2.58e11 8
#> ══════════════════════════════════════════════════════════════════════════