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Avoid filtering in normalization #208

Merged
merged 1 commit into from
May 13, 2022
Merged

Avoid filtering in normalization #208

merged 1 commit into from
May 13, 2022

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scottgigante
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If cells are filtered in this stage, scran throws an error:
error in evaluating the argument 'object' in selecting a method for function 'sizeFactors': 'ncol(x)' is not equal to 'length(clusters)'

@scottgigante
Avoid filtering in normalization
2ce1cb9 
If cells are filtered in this stage, scran throws an error: 
`error in evaluating the argument 'object' in selecting a method for function 'sizeFactors': 'ncol(x)' is not equal to 'length(clusters)'`
@LuckyMD
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LuckyMD commented Jan 19, 2021

Default should be min_counts=1 if this is not kept you can't run total counts normalization as you'd be dividing by zero. I think the solution would be to ensure no 0 count cells are in the dataset. Can't normalize those anyway, no?

@mumichae
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Shall we set min_counts=1 then?

@mumichae mumichae merged commit 3178239 into theislab:main May 13, 2022
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@scottgigante @LuckyMD @mumichae