More robust norm-from-counts

Victorian-Bioinformatics-Consortium · Oct 4, 2016 · 85604ef · 85604ef
1 parent 73095e2
commit 85604ef
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/nesoni/nesoni-r/R/counts.R b/nesoni/nesoni-r/R/counts.R
@@ -53,7 +53,7 @@ read.counts <- function(filename, min.total=0, min.max=0, keep=NULL, norm.file=N
 
     result <- DGEList(counts=counts[good,,drop=F], genes=gene[good,,drop=F])
 
-    mean.lib.size <- exp(mean(log(result$samples$lib.size)))
+    mean.lib.size <- exp(mean(log(pmax(1,result$samples$lib.size))))
 
     if (!have.norm) {
         if (use.tmm) {