# HG changeset patch
# User fubar
# Date 1374903569 14400
# Node ID 755cf582f2c462534c68662cc2998f8676399e56
# Parent  2e35432ee040950f4ad83a107fd99baba3c9c40e
Uploaded

diff -r 2e35432ee040 -r 755cf582f2c4 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:35:23 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:39:29 2013 -0400
@@ -602,6 +602,15 @@
 
   if (doVoom == T) {
       sink('VOOM.log')
+      if (doedgeR == F) {
+         #### Setup DGEList object
+         DGEList = DGEList(counts=workCM, group = group)
+         DGEList = calcNormFactors(DGEList)
+         DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+         comdisp = DGEList\$common.dispersion
+         DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         }
       pdf("VOOM_mean_variance_plot.pdf")
       dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
       dev.off()