# Clarification on Negative Values in Log-Transformed Gene Expression Data

**URL:** <https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902>\
**Category:** Q&A\
**Tags:** omics\
**Created:** [January 12, 2025, 5:53pm UTC](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902 "2025-01-12T17:53:34Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![madhu](https://avatars.discourse-cdn.com/v4/letter/m/a8b319/32.png) [@madhu](https://forum.depmap.org/u/madhu)\
**Post date:** [January 12, 2025, 5:53pm UTC](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902/1 "2025-01-12T17:53:34Z")

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I am working with the DepMap expression datasets, and I have a question regarding the log-transformed values in the **OmicsExpressionProteinCodingGenesTPMLogp1.csv** file.

As per the dataset documentation, the expression values are inferred using RSEM (unstranded mode) and reported after log2 transformation with a pseudo-count of 1. However, I have noticed that some of the log-transformed gene expression values are negative, which seems inconsistent with typical log transformation expectations.

In standard log2 transformations, values of **TPM \> 0** should generally yield non-negative results, particularly when a pseudo-count is added. Could you kindly clarify why negative values appear in the log-transformed expression data? Are there any additional steps or adjustments performed during the transformation that would explain this?

I would greatly appreciate any insights you can provide on this matter.

Thank you for your time and assistance.

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**Author:** ![simz](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/simz/32/440_2.png) [@simz](https://forum.depmap.org/u/simz)\
**Post date:** [January 30, 2025, 10:08pm UTC](https://forum.depmap.org/t/clarification-on-negative-values-in-log-transformed-gene-expression-data/3902/2 "2025-01-30T22:08:23Z")

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Hi,

Please correct me if I’m missing something, but I don’t see any negative values in OmicsExpressionProteinCodingGenesTPMLogp1.csv. However, there are negative values in OmicsExpressionProteinCodingGenesTPMLogp1BatchCorrected.csv, which is our batch-corrected expression matrix.

We are aware that the negative values are an undesirable byproduct of the batch-correcting tool, COMBAT, and we are in the process of evaluating other batch correction tools to address this issue. In the meantime, please refer to the non-batch corrected expression matrix (OmicsExpressionProteinCodingGenesTPMLogp1) if needed.

Thanks!  
Simone