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batch_var doesn't work with vst.flavor = 'v2' #126

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cnk113 opened this issue Feb 10, 2022 · 2 comments
Open

batch_var doesn't work with vst.flavor = 'v2' #126

cnk113 opened this issue Feb 10, 2022 · 2 comments

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@cnk113
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cnk113 commented Feb 10, 2022

Hello,

When I set vst.flavor = 'v2' and batch_var between two different batches I get:
Error in fit$Beta[, "Intercept"] : subscript out of bounds

Thanks,
Chang

@saketkc
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saketkc commented Feb 14, 2022

The current implementation of vst.flavor does not support batch_var and will be added in a future release.

@blasks
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blasks commented May 17, 2023

I'm wondering what the latest on this development is? Are there currently any workarounds to use the method = glmGamPoi_offset and exclude_poisson = TRUE options with batch correction?

Thanks for the great method!

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