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as I can see, the Convert function of SeuratDisk (from h5Seurat to h5ad) will never touch the counts dataset (not-normalised matrix) of the default assay (e.g., "RNA") in a h5Seurat object, as it gives priority to "scale.data" (variable features only) and then "data" (normalised matrix) when filling X.
Is there a way to force such conversion?.. Or maybe use an alternative to SeuratDisk (as no longer supported..)? sceasy seems not a solution, as it picks only a normalised matrix and ignores the rest.
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Hello all -
as I can see, the Convert function of SeuratDisk (from h5Seurat to h5ad) will never touch the counts dataset (not-normalised matrix) of the default assay (e.g., "RNA") in a h5Seurat object, as it gives priority to "scale.data" (variable features only) and then "data" (normalised matrix) when filling X.
Is there a way to force such conversion?.. Or maybe use an alternative to SeuratDisk (as no longer supported..)? sceasy seems not a solution, as it picks only a normalised matrix and ignores the rest.
Thanks a lot in advance for any help
Leo
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