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Function "SelectIntegrationFeatures" For Which Data Assay? #9418

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ForrestGump618 opened this issue Oct 22, 2024 · 0 comments
Open

Function "SelectIntegrationFeatures" For Which Data Assay? #9418

ForrestGump618 opened this issue Oct 22, 2024 · 0 comments

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@ForrestGump618
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ForrestGump618 commented Oct 22, 2024

Dear professors,
Hi!
In the examples demonstrating how to prepare a normalized object list with SCTransform for integration (https://satijalab.org/seurat/reference/prepsctintegration), the provided workflow includes the following code:

if (FALSE) {
# to install the SeuratData package see https://github.com/satijalab/seurat-data
library(SeuratData)
data("panc8")

# panc8 is a merged Seurat object containing 8 separate pancreas datasets
# split the object by dataset and take the first 2 to integrate
pancreas.list <- SplitObject(panc8, split.by = "tech")[1:2]

# perform SCTransform normalization
pancreas.list <- lapply(X = pancreas.list, FUN = SCTransform)

# select integration features and prep step
**features <- SelectIntegrationFeatures(pancreas.list)**
pancreas.list <- PrepSCTIntegration(
  pancreas.list,
  anchor.features = features
)

# downstream integration steps
anchors <- FindIntegrationAnchors(
  pancreas.list,
  normalization.method = "SCT",
  anchor.features = features
)
pancreas.integrated <- IntegrateData(anchors, normalization.method = "SCT")
}

I noticed that the line features <- SelectIntegrationFeatures(pancreas.list) occurs before normalization. Does this imply that SelectIntegrationFeatures utilizes only the raw data, without any normalization?
Thanks!

Qing-yuan Zhuang

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