# HG changeset patch
# User fubar
# Date 1374903793 14400
# Node ID e7733b353702cf03a8cf13319d65fde3f3270fdf
# Parent  755cf582f2c462534c68662cc2998f8676399e56
Uploaded

diff -r 755cf582f2c4 -r e7733b353702 rgedgeR/rgedgeRpaired.xml
--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:39:29 2013 -0400
+++ b/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 01:43:13 2013 -0400
@@ -607,9 +607,10 @@
          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)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         norm.factor = DGEList\$samples\$norm.factors
          }
       pdf("VOOM_mean_variance_plot.pdf")
       dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)