diff --git a/single-cell-analysis/Session_3/Session3.Rmd b/single-cell-analysis/Session_3/Session3.Rmd index d293481..a47c2d8 100644 --- a/single-cell-analysis/Session_3/Session3.Rmd +++ b/single-cell-analysis/Session_3/Session3.Rmd @@ -111,7 +111,7 @@ data <- subset(x=data, subset=nFeature_RNA > 200 & nCount_RNA > quantnCountRNA & print(sprintf("After filtering outliers: %d cells and %d genes", ncol(data), nrow(data))) ``` -##Normalization +## Normalization Now, we will perform sctranform based normalization and visualize the results ```{r} data <- SCTransform(data, method="qpoisson", vars.to.regress = NULL) @@ -199,9 +199,9 @@ sce <- as(sce, "SingleCellExperiment") ## Prep this object for subsequent aggregation analyses (sce <- prepSCE(sce, - cluster_id = "seurat_clusters", # subpopulation assignments - group_id = "sTime", # group IDs - sample_id = "sIndividual", # sample IDs + kid = "seurat_clusters", # subpopulation assignments + gid = "sTime", # group IDs + sid = "sIndividual", # sample IDs drop = TRUE)) # drop all other colData columns nk <- length(kids <- levels(sce$cluster_id)) @@ -350,4 +350,7 @@ DimPlot(batch.integrated, reduction = "tsne", group.by = "Time") DimPlot(batch.integrated, reduction = "tsne", group.by = "batch") ``` +```{r} +sessionInfo() +```