# Count data preprocessing for HAllA

**URL:** <https://forum.biobakery.org/t/count-data-preprocessing-for-halla/304>\
**Category:** HAllA\
**Created:** [March 27, 2020, 10:53am UTC](https://forum.biobakery.org/t/count-data-preprocessing-for-halla/304 "2020-03-27T10:53:48Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Francesca](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/francesca/32/158_2.png) [@Francesca](https://forum.biobakery.org/u/Francesca)\
**Post date:** [March 27, 2020, 10:53am UTC](https://forum.biobakery.org/t/count-data-preprocessing-for-halla/304/1 "2020-03-27T10:53:48Z")

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Hello,

I am new to HAllA and I would like to analyze paired RNA-seq and OTU (16S) data.  
How shall I preprocess the raw counts before running HAllA?

Thank you,  
Francesca

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [April 8, 2020, 6:52pm UTC](https://forum.biobakery.org/t/count-data-preprocessing-for-halla/304/2 "2020-04-08T18:52:43Z")

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Hello Francesca, Sorry for the slow response. I was not sure of the answer so I reached out to the main HAllA developer to check. HAllA uses Spearman correlation for scaling for similarity so the scaling of the data prior to running HAllA is not required.

Thank you,  
Lauren