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During FindVariableFeatures after ALRA output, count slot is empty? #12

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lkqnaruto opened this issue May 14, 2021 · 0 comments
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@lkqnaruto
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Hi

I was trying to use ALRA through Seurat 4.0, and after I normalize the data, and then I run ALRA. I noticed that ALRA will create an new assay, called "alra". I assume under the "alra" assay, the data slot is our "updated" lognormalized data, right? however, the counts slot is empty, which leads to the following warning when I use FindVariableFeatures function:

In FindVariableFeatures.Assay(object = assay.data, selection.method = selection.method, :
selection.method set to 'vst' but count slot is empty; will use data slot instead

Will this cause any trouble in the following analysis?

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