# Z-score for human-microarray and mouse ish-data **URL:** https://community.brain-map.org/t/z-score-for-human-microarray-and-mouse-ish-data/912 **Category:** Technical **Tags:** rna-array, api, analysis, how-to, atlas-human-brain-adult **Created:** [January 25, 2021, 5:39pm UTC](https://community.brain-map.org/t/z-score-for-human-microarray-and-mouse-ish-data/912 "2021-01-25T17:39:31Z") **Posts on this page:** 1 **Showing post:** 9
### 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: [February 28, 2022, 5:14pm UTC](https://community.brain-map.org/t/z-score-for-human-microarray-and-mouse-ish-data/912/9 "2022-02-28T17:14:18Z")
Hi Austin, The [Ivy GAP downloadable data](http://glioblastoma.alleninstitute.org/static/download.html) is FPKM-normalized and _not_ z-scores, and therefore a 0 value means that no RNA for that gene was detected. Here is a [good summary](https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/) of different RNA-seq normalization strategies, but it short, FPKM (fragments per kilobase per million) accounts both for the total number of RNA measured in a sample as well as the gene length. In the heatmap view (e.g, [here](http://glioblastoma.alleninstitute.org/rnaseq/searches?%257B%22search_type%22%253A%22differential%22%252C%22target_features%22%253A%255B298764274%255D%252C%22contrast_features%22%253A%255B309780592%252C309780846%252C309780906%252C298764292%255D%252C%22target_tumors%22%253A%255B%255D%252C%22contrast_tumors%22%253A%255B%255D%252C%22page_num%22%253A0%257D)) I would suggest treating the 0 z-scores either as “NA” or as whatever the smallest non-zero value is. It appears that z is set to 0 whenever the log2 intensity value is 0, which does not make sense, as it always should be negative. More generally, I would recommend using read counts or log normalized FPKM values rather than z-scores whenever dealing with RNA-seq data programatically. Best, Jeremy --- _[View the full topic](https://community.brain-map.org/t/z-score-for-human-microarray-and-mouse-ish-data/912)._