Mercurial > repos > fubar > differential_count_models

changeset 11:e7733b353702 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Sat, 27 Jul 2013 01:43:13 -0400
parents 755cf582f2c4
children aa528c834664
files rgedgeR/rgedgeRpaired.xml
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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)