How to combine gene expression raw scores?

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1

Hello,

I am interested in using AlphaGenome to predict the effects of SNPs on gene expression in disease. I am therefore looking at the effect of multiple SNPs across specific tissue types on single genes.

I am wondering whether there is a good way of aggregating raw scores so that there will be an individual raw score for each gene. My current approach is:

  1. Identify SNPs that have a significant impact on gene expression by identifying those with raw scores 2SD from the mean.
  2. Averaging raw scores across the different specific tissue types i.e. colon tissues
  3. Summing the raw scores of the SNPs that affect the same gene

I understand I could use the quantile score to do weighted sums of the raw scores but I want to be able to compare to real gene expression data, so I don’t want to change the ‘true value’ based on weight.

Please let me know if this would work or if there is a better way of doing this.

Thanks!