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dsb does not run when intersection is False #1

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JHYSiu opened this issue Jan 26, 2023 · 3 comments · May be fixed by #314
Open

dsb does not run when intersection is False #1

JHYSiu opened this issue Jan 26, 2023 · 3 comments · May be fixed by #314
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@JHYSiu
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JHYSiu commented Jan 26, 2023

dsb does not run when half the samples are rna + adt, half the samples are rna only (and no intersection between rna,adt is taken).

fix is to take the intersection of the background: mu.pp.intersect_obs(mdata_bg) prior to mu.prot.pp.dsb

@wlason
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wlason commented Mar 4, 2024

I ran into the same problem in panpipes v0.4.1 and the solution given by @JHYSiu solves the issue.

@wlason
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wlason commented Sep 23, 2024

This is still not fixed as of today @bio-la and I run into the same problem again with another dataset. I will write a fix and create a PR.

@wlason wlason self-assigned this Sep 23, 2024
@deevdevil88
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deevdevil88 commented Sep 24, 2024

@wlason you just need to add an if statement in the preprocess prot script, that when intersect rna,prot is not set, to take the intersect of BG and unfilt mdata obs and then run dsb. Been meaning to add the PR for it as we know the fix but just keep forgetting

@wlason wlason linked a pull request Oct 15, 2024 that will close this issue
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4 participants