# Is smart-seq matrix human multiple cortical areas normalized?

**URL:** <https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703>\
**Category:** Science\
**Tags:** human, atlas-cell-types, rna-seq\
**Created:** [July 7, 2022, 8:12am UTC](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703 "2022-07-07T08:12:52Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![StanDriessens](https://avatars.discourse-cdn.com/v4/letter/s/a6a055/32.png) [@StanDriessens](https://community.brain-map.org/u/StanDriessens)\
**Post date:** [July 7, 2022, 8:12am UTC](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703/1 "2022-07-07T08:12:52Z")

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Hi,

Can someone clarify if the counts in the smart-seq matrices for human cell types have been normalized (CPM)? If not is this dataset also available for normalized values?

Thanks!

Stan

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**Author:** ![jeremyinseattle](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/jeremyinseattle/32/50_2.png) [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)\
**Post date:** [July 18, 2022, 3:36pm UTC](https://community.brain-map.org/t/is-smart-seq-matrix-human-multiple-cortical-areas-normalized/1703/2 "2022-07-18T15:36:25Z")

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According to the readme: “_Gene expression data matrices (matrix.csv): This file csv contains one row for every cell in the dataset and one column for every gene sequenced. The values of the matrix represent total reads (introns + exons) for that gene (column) for that cell (row)._” This means that the data is not normalized. Data can be converted to CPM (or logCPM) using python or R (e.g., with a single line of code in the [scrattch.hicat](https://github.com/AllenInstitute/scrattch.hicat) R library).