Question: GTEX effect sizes and violin plots
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gravatar for ognjen011
7 months ago by
ognjen011170
ognjen011170 wrote:

I am trying to understand the data at GTEX. Searching for data on the particular SNPs I get results in CSV form or browser table e.g. https://gtexportal.org/home/snp/rs1700184

1) Is there any way to get processed information from the violin plots (like medians) in CSV? They only seem available on clicking the links in table.

In CSV by default I only have NES. The explanation is:

Normalized effect size (NES), previously known as the effect size on the portal, is defined as the slope of the linear regression, and is computed as the effect of the alternative allele (ALT) relative to the reference allele (REF) in the human genome reference GRCh37/hg19 (i.e., the eQTL effect allele is the ALT allele). NES are computed in a normalized space where magnitude has no direct biological interpretation.

I understand the general direction of results, but not what is on the Y-axis.

2) How is this normalization ALT to REF performed? Most regressions I looked up were in the space of absolute values. 3) Is this the slope of the line in the same space as the violin plots?

Thanks in advance!

P.S. Pointing me to a good source is the best answer

gtex eqtl expression • 408 views
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