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missing features in SCT scale data of integrated object #3056

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NicolaasVanRenne opened this issue May 23, 2020 · 1 comment
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missing features in SCT scale data of integrated object #3056

NicolaasVanRenne opened this issue May 23, 2020 · 1 comment

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@NicolaasVanRenne
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NicolaasVanRenne commented May 23, 2020 •
edited

Is there a way to calculate SCT scale data of all features, separately?

So I integrate 5 objects using 5000 features, however, many genes are thus still unaccounted for in the [["SCT"]]@scale.data. Which is annoying for downstream analyses using DoHeatmap for example.

Even if I use the all_features setting, it does not seem to include features that have zero counts in one of the 5 objects.
@NicolaasVanRenne NicolaasVanRenne changed the title PrepSCTIntegration: The following x features do not exist in the counts slot: missing features in SCT scale data of integrated object May 23, 2020
@yuhanH
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yuhanH commented Jun 5, 2020

Hi,
You are right. Pearson residues cannot be calculated for the genes that have zero counts across all cells within one individual object. But for the downstream analysis such as heatmap, you can use scale.data in RNA assay.

@yuhanH yuhanH closed this as completed Jun 5, 2020
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@yuhanH @NicolaasVanRenne