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analysis tools #5338

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ClayBirkett opened this issue Feb 20, 2025 · 2 comments
Open

analysis tools #5338

ClayBirkett opened this issue Feb 20, 2025 · 2 comments
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@chris263
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Priority: Critical Issue/PR requires immediate resolution. Type: Bug Issue describes a bug.

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@ClayBirkett
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I have found that most of the analysis tools do not work. One common issue is that the input data has a problem because the tools allow both lists and datasets.
@lukasmueller lukasmueller added Priority: Critical Issue/PR requires immediate resolution. Type: Bug Issue describes a bug. labels Feb 20, 2025
@chris263
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It might be related to this: #5059
It is happening on cassavabase and I couldn't replicate the error. @lukasmueller

@ClayBirkett
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Found one problem where clustering is failing because of prcomp(scale=true). This fails if variance is 0 so removing the scale option fixes this problem. If data is phenotype then scale data if data is genotype then skip this step.

Found another problem where choosing a genotype protocol other than the default protocol is not working.

@ClayBirkett ClayBirkett mentioned this issue Feb 25, 2025
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@lukasmueller @ClayBirkett @chris263