Mercurial > repos > fubar > differential_count_models

diff rgedgeR/rgedgeRpaired.xml @ 11:e7733b353702 draft

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Uploaded
author fubar
date Sat, 27 Jul 2013 01:43:13 -0400
parents 755cf582f2c4
children aa528c834664
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--- 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)