# What is the format of gene expression value in allen human brain atlas?

**URL:** <https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830>\
**Category:** Science\
**Tags:** transcriptomics, analysis, atlas-human-brain-adult\
**Created:** [September 7, 2022, 6:56am UTC](https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830 "2022-09-07T06:56:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jiwieli](https://avatars.discourse-cdn.com/v4/letter/j/dfb087/32.png) [@jiwieli](https://community.brain-map.org/u/jiwieli)\
**Post date:** [September 7, 2022, 6:56am UTC](https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830/1 "2022-09-07T06:56:49Z")

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hello, allen institute.  
I am fairly new to working with transcriptomics data. I download human brain data from [Microarray Data Download :: Allen Brain Atlas: Human Brain](http://human.brain-map.org/static/download). I want to do some differential gene expression analysis between diffrent brain regions using ready-made R package such as “limma”. But i did not find any apparent description of the data format. In MicroarrayExpression.csv, data is count (after log2)? or TPM,FPKM (after normalization)?  
Thanks!

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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:** [September 8, 2022, 3:29pm UTC](https://community.brain-map.org/t/what-is-the-format-of-gene-expression-value-in-allen-human-brain-atlas/1830/2 "2022-09-08T15:29:55Z")

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Hi @jiwieli. We have a white paper describing how the data was normalized ([Microarray Data Normalization](http://help.brain-map.org/download/attachments/2818165/Normalization_WhitePaper.pdf?version=1&modificationDate=1361836502191&api=v2)), but essentially each number is a value representing the amount of light emitted from the indicated probe on a specific microarray chip. These values are quantitative (e.g., you can believe that a two-fold change in value really means a two-fold change in gene expression), but don’t represent absolute expression levels in the way that you get with RNA-seq data. The values in the downloaded table are log normalized. There are a few other Community Forum posts on this topic (type “Microarray” in the search box) if you are interested in more information.