Normalise batch effects for Percent Spliced In (PSI) matrice

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5.9 years ago

ZheFrench ▴ 590

The exon-inclusion ratio, also known as percent spliced in (PSI), is a popular statistic for measuring alternative splicing events. How do you correct batch effects for matrice with this kind of values ?

For gene expression, you can use combat or sva, but for psi (value between -1;1) ? Any ideas ?

combat sva splicing • 1.9k views

ADD COMMENT • link updated 9 months ago by Yogi ▴ 70 • written 5.9 years ago by ZheFrench ▴ 590

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Any luck with this? I have PSI values as well, although they are all between 0 and 1. I need a way to estimate any number of unknown batch effects and produce a batch-corrected PSI matrix.

ADD REPLY • link 4.7 years ago by eggerj ▴ 40

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Nope didn't find a solution for this one.Good Luck.

ADD REPLY • link 4.7 years ago by ZheFrench ▴ 590

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Did you end up figuring this out?

If so, what was your general methodology? Would love to discuss.

ADD REPLY • link 9 months ago by Yogi ▴ 70

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