Mercurial > repos > yhoogstrate > edger_with_design_matrix

diff edgeR_Differential_Gene_Expression.xml @ 122:7bb87a6bc4d5 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc
author yhoogstrate
date Wed, 16 Dec 2015 11:15:18 -0500
parents 6c90a67a13fa
children
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--- a/edgeR_Differential_Gene_Expression.xml	Mon Dec 14 05:10:49 2015 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Dec 16 11:15:18 2015 -0500
@@ -288,6 +288,11 @@
   if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
     write("Calculating MDS plot (logFC method)",stdout())
     n_dim <- nrow(dge\$samples)
+    
+    if(n_dim >= nrow(dge\$counts)) {
+      n_dim <- 3
+    }
+    
     mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
     dev.off()# Kill it