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madsen-lab / valiDrops

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"Error: psi values too close each other" with segmented 2.0-1 #14

Closed benduc closed 4 months ago

benduc commented 9 months ago

Hi, Thanks for developing this great tool. Since the package segmented was updated to 2.0-1, there are several samples that crash when running

valiDrops(seurat, rank_barcodes = FALSE)

due to the error "Error: psi values too close each other. Please change (decreases number of) starting values".

This is solved when reinstalling segmented 1.6.4.

JesperGrud commented 9 months ago

Hi.

Thank you for your interest in using valiDrops. That sounds curious. We will try to reproduce with different versions of segmented and get back to you as soon as possible. However, it may be some time. In the mean time I would advise you to use 1.6.4

yesitsjess commented 9 months ago

I'm also having this issue but only for 1/5 of my datasets (so far). I will try installing an older version of segmented too

ashipde commented 6 months ago

I too encounter this issue, which seems to be solved by reducing npsi to 2 (default is 3). I haven't tried downgrading segmented to 1.6 from the current version, 2.0. I wish the documentation had more information on parameters like npsi and mito.max so one could understand the consequences of changing them from default values.

ashipde commented 6 months ago

This issue appears to be fixed in v1.1.0.

JesperGrud commented 4 months ago

Closing as this error is also being evaluated in issue #17