# HG changeset patch
# User yhoogstrate
# Date 1400768099 14400
# Node ID 47eadcd9e4b89635f8c4b37c27b9651827459569
# Parent  00b9ceac43322728bdd5a6b775cc7b2f3b5b7c8e
Uploaded

diff -r 00b9ceac4332 -r 47eadcd9e4b8 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:10:03 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:14:59 2014 -0400
@@ -280,9 +280,10 @@
     
     if(output_heatmap_plot != "/dev/null") {
       pdf(output_heatmap_plot)
-      etable2 <- topTags(lrt, n=100)\$table
+      etable2 <- topTags(lrt, n=100)$table
       order <- rownames(etable2)
-      heatmap(t(cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA),log=TRUE))
+      cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
+      heatmap(t(cpm_sub))
       dev.off()
     }
   }