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:

• One sample per row
• One molecule per column
• Expression values as numbers, empty cells, NA, or NaN

Example table

📄 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	...

Rules

Header (first row)

Sample	A0A1B0GTW7	H3BV60	O14717	...

• The header is the very first line of the file. These contain column names (e.g. UniProt IDs)
• There is no specific requriements for the first cell (A1). You can also leave it empty if preferred.
• Every other column name must be a valid molecule ID (UniProt, Ensembl, CHEBI, or InChI).
• Only one type of ID can be used per file — mixing ID types is not allowed.
• No empty cells in the header.

First column

• Contains sample names (e.g. Sample 1, Patient_A).
• Each sample name must be unique and non-empty.

Sample
Patient A
Patient B
Patient C
...

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!

Statistics CSV-file(s)