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Expression Matrix CSV-file
ℹ️ What is an expression matrix?
An expression matrix is a table where each row represents a measured feature - a gene, protein, or metabolite - and each column represents a sample. Each cell contains a numeric value reflecting the abundance of that feature in that sample.
How to format the expression matrix before uploading to Omics Studio
Your file must be a CSV file with:
Option A
- One sample per row
- One molecule ID per column
Option B
- One molecule ID per row
- One sample per column
Relevant for both options
- Molecule IDs must be a valid (
UniProt,Ensembl,CHEBI, orInChI). Only one type of ID can be used per file – mixing ID types is not allowed. - Each sample name must be unique and non-empty.
- No empty cells in first row or column (besides A1).
- There is no specific requriements for the first cell (A1). You can also leave it empty if preferred.
Example of option A
📄 Expression Matrix (.csv)
| Sample | A0A1B0GTW7 | H3BV60 | O14717 | ... |
|---|---|---|---|---|
| Sample 1 | 10.1410167828492 | 9.93186549252307 | 6.69890691314978 | ... |
| Sample 2 | 9.73564973428653 | 8.08565905751542 | 12.5898915913406 | ... |
| Sample 3 | 11.5021226052126 | 10.7956844176007 | 8.75086505276381 | ... |
| Sample 4 | 10.1410167828492 | 9.93186549252307 | 6.69890691314978 | ... |
Example of option B
📄 Expression Matrix (.csv)
| ID | Sample 1 | Sample 2 | Sample 3 | ... |
|---|---|---|---|---|
| A0A1B0GTW7 | 10.1410167828492 | 9.73564973428653 | 11.5021226052126 | ... |
| H3BV60 | 9.93186549252307 | 8.08565905751542 | 10.7956844176007 | ... |
| O14717 | 6.69890691314978 | 12.5898915913406 | 8.75086505276381 | ... |
| P05067 | 5.95454521872124 | 7.86046505274539 | 4.87546291318788 | ... |
Expression values
- Each expression value must be a number or the text
NA. - Empty cells and
NAare all treated asNaNvalues. - Any other text (e.g.
missing,abc) will cause an error.
| 10.1410167828492 | NA | 6.69890691314978 | ... |
| 9.73564973428653 | 8.08565905751542 | 12.5898915913406 | ... |
| 11.5021226052126 | 10.7956844176007 | ... | |
| NaN | 9.93186549252307 | 6.69890691314978 | ... |
💡 Good to know
✅ You can use both types of decimal separators (e.g. 10.53 or 10,53).
❌ Thousand separators are not allowed!