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Which assay and slot does IntegrateData uses #7575

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Rohit-Satyam opened this issue Jul 15, 2023 · 2 comments
Closed

Which assay and slot does IntegrateData uses #7575

Rohit-Satyam opened this issue Jul 15, 2023 · 2 comments

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@Rohit-Satyam
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Rohit-Satyam commented Jul 15, 2023 •
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I have a small query now that I am running Integration after running RunALRA function. Does IntegrateData uses "RNA" assay and it's data slot while running IntegrateData function or does it use default assay's data slot (which RunALRA sets to "alra")? Since I couldn't find any tutorial on how can one use both ALRA and Seurat together for integrating imputed data as we discuss in issues here and here, I was tempted to ask here. I am planning to use "logNormalization". And I have 4 samples where DefaultAssay is "alra" (because I carried out imputation) and 1 reference atlas MCA which has DefaultAssay as "RNA".
@Rohit-Satyam
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@troels @pmarks @mxposed @zeehio Please help.

@Gesmira
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Gesmira commented Jul 21, 2023

Hi,
In FindIntegrationAnchors, you can set the assay that will be used per object. If you don't specify the assay, it will take the DefaultAssay per object.

@Gesmira Gesmira closed this as completed Jul 21, 2023
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@Rohit-Satyam @Gesmira