Human Brain Atlas: Microarray Data Download

Download Page

The available options for downloading the microarray data include downloading the entire normalized data set for each brain by clicking on the text links in the box (as seen in the image below), or using the XML or CSV link to download the individual raw microarray data files.

Download of RNASeq data for 240 samples is also available.

You can also download the archived normalized microarray expression values that utilized an earlier normalization method from prior to the March 2013 data release.

Hello Allen Brain team,

The Human Brain microarray atlas is a great resource for exploring gene expression in the brain! I was wondering how to download expression values normalized across all the brains(donors) which called Z-score that I can explore through API. However, I cannot find the download link. In the download page, the zip files seems only contain the normalized values for that donor. How can I download the Z-score matrix files? Can you please help me with this?


Hi @jinkuizhu,

The short answer is that you cannot download all the z-scores at once, but you have two choices to get them:

  1. If you are looking at a search result in the app when z-scores are currently being shown, then you can download data for your current view by clicking on the download data button at the bottom of the page.
  2. You can download the normalized values and then calculate them yourself for each probe-set independently as [x-mean(x)]/[stdev(x)], where x is the values for a given gene across all microarray samples.

There are several forum topics (i.e., this one) related to idiosyncrasies of how z-scores are calculated in different situations and personally I’d recommend using the normalized values instead, but if you want z scores, it should be a straightforward and computationally inexpensive calculation.



Thank you very much! That helps a lot.