# Which one of the expression data is proper for machine learning?

**URL:** <https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367>\
**Category:** Q&A\
**Tags:** genetic-screens, omics, data\
**Created:** [June 25, 2024, 6:41am UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367 "2024-06-25T06:41:38Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![SongSong](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@SongSong](https://forum.depmap.org/u/SongSong)\
**Post date:** [June 25, 2024, 6:41am UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367/1 "2024-06-25T06:41:38Z")

</div>

Hi, thank you for your effort in launching the newest dataset version 2024Q2.  
But I’m a little confused about the two kinds of gene expression data: original and batch normalized.  
If I want to use the gene expression data for the machine learning model training, which one should I use?  
I checked that the original has some 0 values and the batch normalized dataset doesn’t have 0 but negative values.  
Can anyone recommend the dataset?

---

<div class="post-metadata">

**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:** [June 25, 2024, 3:38pm UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367/2 "2024-06-25T15:38:38Z")

</div>

Hi,

I’d recommend using the batch-corrected data, as we are planning to phase out the non-batch corrected data in the future. For details, please see the pdf attached at the end of the [24Q2 release announcement](https://forum.depmap.org/t/announcing-the-24q2-release/3312).

Thanks,  
Simone

---

<div class="post-metadata">

**Author:** ![SongSong](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@SongSong](https://forum.depmap.org/u/SongSong)\
**Post date:** [September 3, 2024, 5:55am UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367/3 "2024-09-03T05:55:03Z")

</div>

Dear Simone,

Hi, thank you for your kind reply.  
Although I already selected your answer as the solution to this question, I have one more question about the dataset; not expression, but copy number.  
To my knowledge, the previous version of copy number(CN) values was provided with the log2-transformed version.  
But from the 24Q2, the relative copy number matrix is no longer log2 transformed.  
If I want to use CN data with the gene expression data which is log2-transformed TPM value for the machine learning data, should I use PortalOmicsCNGeneLog2.csv for the consistent range of value or use OmicsCNGene.csv to keep the original data?

Thank you for reading this question.  
I look forward to your reply.

Sincerely,  
Songyeon

---

<div class="post-metadata">

**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:** [September 3, 2024, 3:19pm UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367/4 "2024-09-03T15:19:03Z")

</div>

Hi Songyeon,

PortalOmicsCNGeneLog2 is the log2-transformed version of OmicsCNGene. They are essentially the same data, so as far as I know, you may use either depending on what you need for your particular analysis.

Best,  
Simone

---

<div class="post-metadata">

**Author:** ![SongSong](https://avatars.discourse-cdn.com/v4/letter/s/a9a28c/32.png) [@SongSong](https://forum.depmap.org/u/SongSong)\
**Post date:** [September 4, 2024, 2:10am UTC](https://forum.depmap.org/t/which-one-of-the-expression-data-is-proper-for-machine-learning/3367/5 "2024-09-04T02:10:14Z")

</div>

Thank you for your kind reply.  
I’ll think about it a little more. 🙂