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I am using SCT to normalize my Xenium data and I have lot of cells, so I was going to increase the ncells parameter to be about 10% of the total cells I am analyzing to get a better NB model. Does any on know if the ncells parameter just takes the first n cells in the Seurat metadata or does it randomly shuffle and select n cells? I am worried that there would be a bias in the NB model if it is the former. Thanks!
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Hi All,
I am using SCT to normalize my Xenium data and I have lot of cells, so I was going to increase the ncells parameter to be about 10% of the total cells I am analyzing to get a better NB model. Does any on know if the ncells parameter just takes the first n cells in the Seurat metadata or does it randomly shuffle and select n cells? I am worried that there would be a bias in the NB model if it is the former. Thanks!
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