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jmbreda / Sanity

Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
GNU General Public License v3.0
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About pbmc3k data in Sanity #9

Open millersan opened 2 years ago

millersan commented 2 years ago

Dear authors, Please accept my sincere thanks for providing such a useful tool. Could you provide a vignette about the Sanity using in Seurat or Scanpy? I have tried the pbmc3k data, but it looks like all values are negative numbers, so it can't load by the Seurat pipeline. Best, Miller

ptdtan commented 2 years ago

The values might be in log scale. Did you try to exponential the values before import those to Seurat?

maximelepetit commented 2 years ago

I think you need to load the normalize matrix (with negative values) to the "data" slot in Seurat object. It work for me with another dataset .

millersan commented 2 years ago

I think you need to load the normalize matrix (with negative values) to the "data" slot in Seurat object. It work for me with another dataset .

The values might be in log scale. Did you try to exponential the values before import those to Seurat?

Thanks a lot!

maximelepetit commented 2 years ago

see #17