fixes

Author: johanneskoester

scripts/batch-effect-removal.R

@@ -28,6 +28,6 @@ colnames(design) <- snakemake@params[["model_variables"]]
 saveRDS(design, file=snakemake@output[["design_matrix"]])
 
 # remove batch effects based on variables
-batch.removed <- removeBatchEffect(normcounts(sce), covariates=model.vars[, snakemake@params[["model_variables"]]])
-normcounts(sce) <- batch.removed
+batch.removed <- removeBatchEffect(logcounts(sce), covariates=model.vars[, snakemake@params[["model_variables"]]])
+logcounts(sce) <- batch.removed
 saveRDS(sce, file=snakemake@output[["sce"]])

scripts/hvg-correlation.R

@@ -42,7 +42,7 @@ dev.off()
 # choose significantly correlated genes
 chosen <- unique(c(var.cor$gene1[sig.cor], var.cor$gene2[sig.cor]))
 # get normalized expressions
-norm.exprs <- exprs(sce)[chosen,,drop=FALSE]
+norm.exprs <- logcounts(sce)[chosen,,drop=FALSE]
 
 
 # plot heatmap