# DESeq2 with single cell data - do cells from same sample get treated independently during analysis?

**URL:** https://help.galaxyproject.org/t/deseq2-with-single-cell-data-do-cells-from-same-sample-get-treated-independently-during-analysis/6342
**Category:** usegalaxy.eu support
**Tags:** single-cell
**Created:** [July 9, 2021, 10:27am UTC](https://help.galaxyproject.org/t/deseq2-with-single-cell-data-do-cells-from-same-sample-get-treated-independently-during-analysis/6342 "2021-07-09T10:27:30Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![carolyn\_nielsen](https://avatars.discourse-cdn.com/v4/letter/c/edb3f5/32.png) [@carolyn\_nielsen](https://help.galaxyproject.org/u/carolyn_nielsen)
#### Post date: [July 9, 2021, 10:27am UTC](https://help.galaxyproject.org/t/deseq2-with-single-cell-data-do-cells-from-same-sample-get-treated-independently-during-analysis/6342/1 "2021-07-09T10:27:30Z")

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I have plate-based single cell data from 7 vaccinees from two different dosing regimens (SmartSeq v4, Nextera Libraries). These were run through a pipeline leading to FeatureCounts prior to DESeq2 described here: [DEseq2 error with different numbers of rows - #12 by carolyn\_nielsen](https://help.galaxyproject.org/t/deseq2-error-with-different-numbers-of-rows/5888/12)

I have just discussed this data with a colleague though and he wondered whether DESeq2 properly controlled for or pseudo-pooled cells from within the same vaccinee sample, or whether they were (incorrectly) treated as independent samples and inflating the number of significant differences between the two groups.

I had assumed that DESeq2 controlled for cells coming from the same vaccinee sample given there is a single FeatureCounts collection input per vaccinee. Is this correct? Is DESeq2 an appropriate tool for single cell analyses?

Each collection selected below for input to DESeq contains a FeatureCount tabular file per cell from that vaccinee (i.e 37-88 FeatureCount files per collection depending on number of cells obtained from each vaccinee):

 ![image](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/1/15865cf509ea0570ae34be30c7193d157e0a98de.png)