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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 integratepancreas.list<- SplitObject(panc8, split.by="tech")[1:2]
# perform SCTransform normalizationpancreas.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 stepsanchors<- 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
The text was updated successfully, but these errors were encountered:
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:
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
The text was updated successfully, but these errors were encountered: