# Issue with normalization of seurat object

**URL:** <https://community.brain-map.org/t/issue-with-normalization-of-seurat-object/2949>\
**Category:** Technical\
**Created:** [January 22, 2024, 5:23pm UTC](https://community.brain-map.org/t/issue-with-normalization-of-seurat-object/2949 "2024-01-22T17:23:59Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![tdaf](https://avatars.discourse-cdn.com/v4/letter/t/13edae/32.png) [@tdaf](https://community.brain-map.org/u/tdaf)\
**Post date:** [January 22, 2024, 5:23pm UTC](https://community.brain-map.org/t/issue-with-normalization-of-seurat-object/2949/1 "2024-01-22T17:23:59Z")

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Hello!  
Firstly, thank you for creating and sharing such a great resource

I am interested in creating a Seurat object out of the Mouse Whole Cortex and Hippocampus 10x RNAseq data, specifically only interested in the hippocampus cells (‘HIP’)

I managed to access and filter for HIP the gene expression matrix.csv file using an SCC to surpass the size memory limitations.  
However, when I try to normalize the data in the standard Seurat workflow, I come across this error:

> hp\_allen ← NormalizeData(hp\_allen, assay = “RNA”)  
> Performing log-normalization  
> 0% 10 20 30 40 50 60 70 80 90 100%  
> [----|----|----|----|----|----|----|----|----|----|  
> \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*|  
> Error: All cells in the object being added must match the cells in this object

I am using R version 4.2.3 (2023-03-15)

Any insight on what I might be doing wrong?

Thank you!

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**Author:** ![Changkyu\_Lee](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/changkyu_lee/32/1454_2.png) [@Changkyu\_Lee](https://community.brain-map.org/u/Changkyu_Lee)\
**Post date:** [February 2, 2024, 8:41pm UTC](https://community.brain-map.org/t/issue-with-normalization-of-seurat-object/2949/2 "2024-02-02T20:41:07Z")

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Sorry for the late reply…

Seurat v5 provides a way not to load the whole data into memory and do the analysis. Please take a look here for the detail.

[https://satijalab.org/seurat/articles/seurat5\_sketch\_analysis](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fseurat5_sketch_analysis&data=05%7C02%7C%7C231a5fdacbf744ea6e7e08dc2408ea65%7C32669cd6737f4b398bddd6951120d3fc%7C0%7C0%7C638424867931244378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=AVad3xPAijSZEnTliwnnboGV6mn7LwIYU6vQjfFz4WE%3D&reserved=0)