# Batch effect control in RNA-seq count data?

**URL:** <https://forum.depmap.org/t/batch-effect-control-in-rna-seq-count-data/2843>\
**Category:** Q&A\
**Created:** [September 29, 2023, 6:52pm UTC](https://forum.depmap.org/t/batch-effect-control-in-rna-seq-count-data/2843 "2023-09-29T18:52:46Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![phytomind](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/phytomind/32/257_2.png) [@phytomind](https://forum.depmap.org/u/phytomind)\
**Post date:** [September 29, 2023, 6:52pm UTC](https://forum.depmap.org/t/batch-effect-control-in-rna-seq-count-data/2843/1 "2023-09-29T18:52:46Z")

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Hello DepMap,

I was wondering how the batch effect was controlled in the latest RNA-seq pipeline. Currently, you can download two different RNA-seq readouts; log-transformed TPM vs RSEM expected count. I was more interested in the RSEM count to use it as a count matrix input in DESeq2. But I just wanted to check if it makes sense to do that without knowing batch info, because the raw count might not have been controlled for batch effect. Thanks.

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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:** [November 16, 2023, 8:28pm UTC](https://forum.depmap.org/t/batch-effect-control-in-rna-seq-count-data/2843/2 "2023-11-16T20:28:45Z")

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Hi,

Apologies for the late reply! Currently DepMap doesn’t do any batch effect correction for the RNAseq data.

Thanks,  
Simone