confusion of normalization method for sQTL input date prepare

[tianwen0003]

Hi

I noticed you chose to normalize intron usage of one sample by RINT cross all intron rather than normalize one intron cross all samples as GTEx eQTL did, I really don’t understand the reason for this. I would be grateful if you can provide some explain to help my understanding?

Thanks

[goldenflaw]

I'm afraid there is no good explanation for this. It just works empirically, i.e. it yields more qtls at the same FDR. I suspect that it might help get rid of outliers.

Best, Yang

On Mon, Dec 19, 2022, 01:56 tianwen0003 @.***> wrote:

Hi

I noticed you chose to normalize intron usage of one sample by RINT cross all intron rather than normalize one intron cross all samples as GTEx eQTL did, I really don’t understand the reason for this. I would be grateful if you can provide some explain to help my understanding?

Thanks

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