Mercurial > repos > fubar > differential_count_models

changeset 10:755cf582f2c4 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 01:39:29 -0400
parents 2e35432ee040
children e7733b353702
files rgedgeR/rgedgeRpaired.xml
diffstat 1 files changed, 9 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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()