Reproducing r-score correlations in Allen Human Brain Atlas

Science
, , , ,
2

Hi @jenniferhu04,

This question has come up before, prior to the start of the community forum, and I’ve copied the answer here:

The issue is that the defaults for viewing microarray data do not match with the data that is used for calculating correlations. The correlations are calculated using the log2 intensity values on a sample-by-sample resolution. Gain access to this data, you will need to do the following:

  1. Go to your link: Microarray Data :: Allen Brain Atlas: Human Brain
  2. Turn Filter Heatmap: On (located just below the heatmap)
  3. Set Resolution = Samples
  4. Change the Color Map to log2 intensity
  5. THEN click “download the data” and save these data
  6. When you calculate the correlations on these data they should match with the value listed on the website.

If this doesn’t solve your problem or you still have questions, please reply to this thread. Good luck in your research!

Best,
Jeremy