# HG changeset patch
# User yhoogstrate
# Date 1400768858 14400
# Node ID d9c9caf4e182290ca6b8a9a068ce67060470183b
# Parent  1b8ecb48f6e7b6e224cb0707e1734aee66af4aa6
Uploaded

diff -r 1b8ecb48f6e7 -r d9c9caf4e182 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:16:58 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:27:38 2014 -0400
@@ -277,15 +277,15 @@
       ## change e into epsilon somehow
       dev.off()
     }
-    
-    if(output_heatmap_plot != "/dev/null") {
-      pdf(output_heatmap_plot)
-      etable2 <- topTags(lrt, n=100)\$table
-      order <- rownames(etable2)
-      cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
-      heatmap(t(cpm_sub))
-      dev.off()
-    }
+  }
+  
+  if(output_heatmap_plot != "/dev/null") {
+    pdf(output_heatmap_plot)
+    etable2 <- topTags(lrt, n=100)\$table
+    order <- rownames(etable2)
+    cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
+    heatmap(t(cpm_sub))
+    dev.off()
   }
   
   ##output_hierarchical_clustering_plot = args[13]
@@ -332,11 +332,11 @@
 		</data>
 		
 		<data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
-			<filter>("make_output_R" in outputs)</filter>
+			<filter>("make_output_RData_obj" in outputs)</filter>
 		</data>
 		
-		<data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output" >
-			<filter>("make_output_RData_obj" in outputs)</filter>
+		<data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
+			<filter>("make_output_R" in outputs)</filter>
 		</data>
 	</outputs>