Fix astrocyte logcounts

code/download-raw-data.R

@@ -71,8 +71,10 @@ rownames(astro_sce) <- rowData(astro_sce)$SYMBOL
 astro_sce <- astro_sce[rownames(c2l_astrocytes_sce), ]
 
 # Permute the cells into the same ordering.
-c2l_astrocytes_sce <- c2l_astrocytes_sce[, colnames(astro_sce)]
-logcounts(astro_sce) <- assay(c2l_astrocytes_sce, "X")
+# We used to try to use the transformed data but it is not logcounts
+# and therfore cannot be used in this way.
+# c2l_astrocytes_sce <- c2l_astrocytes_sce[, colnames(astro_sce)]
+# logcounts(astro_sce) <- assay(c2l_astrocytes_sce, "X")
 
 saveRDS(astro_sce, here::here("data", "raw_data", "astrocyte.rds"))
 

code/prep-astrocyte.R

@@ -17,6 +17,10 @@ astrocyte <- readRDS(args$raw_data)
 
 colLabels(astrocyte) <- as.factor(colLabels(astrocyte))
 
+clusters <- quickCluster(astrocyte)
+astrocyte <- computeSumFactors(astrocyte, clusters = clusters)
+astrocyte <- logNormCounts(astrocyte)
+
 astrocyte <- runPCA(astrocyte)
 astrocyte <- runTSNE(astrocyte, dimred = "PCA")
 astrocyte <- runUMAP(astrocyte, dimred = "PCA")