Expression Matrix CSV-file

What is an expression matrix?

An expression matrix is a table that shows how much of each molecule (gene, protein, or metabolite) is found in each 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, or InChI). 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 NA are all treated as NaN values.
• 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!