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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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confusion of normalization method for sQTL input date prepare #223

Open tianwen0003 opened 1 year ago

tianwen0003 commented 1 year ago

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 commented 1 year ago

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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