Statistics CSV-file

What is a statistics file?

A statistics file contains the results of comparisons between groups (e.g. treated vs control) for each molecule, such as fold changes and p-values.

How to format the statistics file before uploading to Omics Studio

Your file must be a CSV file with:

ID	Comparison	Fold_change	Log2_Fold_change	p_value	Adjusted_p_value	...

• The following columns are required (case-insensitive):

  • ID
  • Comparison
  • Fold Change
  • Log2 Fold change
  • P-value
  • Adjusted P-value

• Optional: you can add extra columns (e.g., metadata, annotations, etc.)

Example table

📄 Statistics (.csv)

ID	Comparison	Fold_change	Log2_Fold_change	p_value	Adjusted_p_value	...
A0A1B0GTW7	Treated vs Control	1.45	0.84	0.011	0.044	...
H3BV60	Treated vs Control	-0.84	-0.25	0.091	0.102	...
O14717	Treated vs Control	0.22	-2.18	0.943	0.121	...
P05067	Treated vs Control	1.12	0.17	0.051	0.943	...

How Molecule IDs and Comparisons must be paired

• Only one type of molecule ID (UniProt, Ensembl, CHEBI, or InChI) can be used per file – mixing molecule ID types is not allowed.
• Each row represents a unique combination of a molecule ID and a Comparison combination.
  • The same molecule ID (e.g., H3BV60) can appear in multiple comparisons – for example, X vs Y and X vs Z.
  • However, each molecule ID + comparison pair must be unique. That means you cannot have two rows with the same molecule ID for the same comparison (e.g., two entries for H3BV60 in X vs Y).

Example

📄 Statistics (.csv)

ID	Comparison	...
A0A1B0GTW7	Treated vs Control	...
H3BV60	Treated vs Control	...
A0A1B0GTW7	Unreated vs Treated	...
H3BV60	Untreated vs Treated	...

⚠️ If uploading several statistics files

Make sure that there is no dublicates across files, where the same ID and Group Comparison is mentioned. E.g. If UniProt ID O14717 combined with comparison X vs Y is in several files, you will not be able to create a study (including both files).

Show example

Statistics CSV file 1

ID	Comparison	Fold_change	p_value	Adjusted_p_value
O14717	X vs Y	1.23	0.004	0.015
H3BV60	X vs Y	-0.88	0.041	0.089
A0A1B0GTW7	X vs Z	0.35	0.120	0.200
Q8IZX4	A vs B	-1.12	0.009	0.030

Statistics CSV file 2

ID	Comparison	Fold_change	p_value	Adjusted_p_value
O14717 (❌ duplicate)	X vs Y (❌ duplicate)	1.19	0.006	0.020
H3BV60	Z vs X	0.91	0.033	0.075
A0A1B0GTW7 (❌ duplicate)	X vs Z (❌ duplicate)	0.40	0.098	0.170
Q9XYZ1	A vs C	-0.51	0.210	0.310

How to fix it:
Remove the duplicates from either Statistics 1 or Statistics 2 before uploading again.

General overview of the columns

If in doubt how to the rules apply to the different mandatory columns, you can learn more in the following.

Molecule ID columns

• Must contain molecule identifiers (e.g. UniProt, Ensembl, CHEBI, or InChI).
• Only one ID type is allowed per file.
• No empty cells are allowed in this column.
• Each ID must be unique.

Example

ID
A0A1B0GTW7
H3BV60
O14717
...

Comparison columns

• Each value must represent a unique pairwise comparison, formatted as:

Examples:

• Treated vs Control
• Sample_A vs Sample_B
• You must add vs between the two.
• Format is case-insensitive (x vs y = X vs Y).
• The two parts must be different (e.g. X vs X is invalid).
• No empty cells are allowed in this column.

Example

Comparison
Treated vs Control
ConditionA vs ConditionB
Group1 vs Group2

Numeric columns

• The following columns must contain numeric values (or NA):
• Fold_change
• p_value
• Adjusted_p_value
• Empty cells and NA are treated as missing values.
• Any other text (e.g. missing, null, none) will cause an error.

Example

Fold_change	p_value	Adjusted_p_value
1.45	0.0025	0.011
-0.84	0.045	0.091
0.22	NA	NA

Additional columns

• You may include as many extra columns (e.g. gene names, annotations, or statistics) as you like.
• These are not part of the validation criteria in Omics Studio when uploading, but must still have a non-empty header.
• Empty values are allowed in these columns.

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💡 Good to know

✅ Underscores, spaces, and hyphens are ignored (p value, p-value, or p_value are all valid). ✅ Plural “s” at the end is ignored (comparisons = comparison).
✅ Decimal separators can be either . or ,.
❌ Thousand separators are not allowed.
❌ Empty headers or missing required columns will cause upload errors.