# HG changeset patch
# User yhoogstrate
# Date 1401268308 14400
# Node ID c6e787bb605ce76efc8a3acaaa2057c0fb682955
# Parent  af6e8c45d1429594cadd28fadc4b1605b71fc61d
Uploaded

diff -r af6e8c45d142 -r c6e787bb605c edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Thu May 22 10:38:19 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Wed May 28 05:11:48 2014 -0400
@@ -102,7 +102,7 @@
 			<option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
 			<option value="make_output_heatmap_plot">Heatmap</option>
 			
-			<option value="make_output_R">R stdout</option>
+			<option value="make_output_R_stdout">R stdout</option>
 			<option value="make_output_RData_obj">R Data object</option>
 		</param>
 	</inputs>
@@ -125,7 +125,7 @@
 output_count_edgeR                  = args[5]
 output_cpm                          = args[6]
 
-output_xpkm                         = args[7]											##FPKM file - yet to be implemented
+output_xpkm                         = args[7]							##FPKM file - yet to be implemented
 
 output_raw_counts                   = args[8]
 output_MDSplot                      = args[9]
@@ -160,6 +160,7 @@
 
 
 columns &lt;- match(rownames(design_matrix),colnames(expression_matrix))
+columns &lt;- columns[!is.na(columns)]
 read_counts &lt;- expression_matrix[,columns]
 
 
@@ -336,7 +337,7 @@
 		</data>
 		
 		<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>
+			<filter>("make_output_R_stdout" in outputs)</filter>
 		</data>
 	</outputs>