# Question on handling sc.pp.regress\_out() in scanpy

**URL:** <https://discourse.scverse.org/t/question-on-handling-sc-pp-regress-out-in-scanpy/1340>\
**Category:** scanpy\
**Created:** [April 24, 2023, 5:09pm UTC](https://discourse.scverse.org/t/question-on-handling-sc-pp-regress-out-in-scanpy/1340 "2023-04-24T17:09:54Z")\
**Posts on this page:** 1\
**Page:** 1

<div class="post-metadata">

**Author:** ![JuliaChristiaanse](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/juliachristiaanse/32/630_2.png) [@JuliaChristiaanse](https://discourse.scverse.org/u/JuliaChristiaanse)\
**Post date:** [April 24, 2023, 5:09pm UTC](https://discourse.scverse.org/t/question-on-handling-sc-pp-regress-out-in-scanpy/1340/1 "2023-04-24T17:09:54Z")

</div>

Hi everyone!

I am a bioinformatics student fairly new to the scanpy universe and I have a question regarding the sc.pp.regress\_out() function.  
I scowered the interned for answers and I thought I might as well try here.  
I am wondering why scanpy’s pbmc3k tutorial (and many similar ones) use ‘total\_counts’ as well as ‘pct\_counts\_mt’ when regressing out data. Why not just use ‘pct\_counts\_mt’? Or any other specific unwanted variation in your dataset (cell cycle, for example). Will regressing out total\_counts not affect all of the dataset, or am I looking at this all wrong?

Me and my supervisor are grateful for your reply! 🙂