Mercurial > repos > fubar > differential_count_models

diff rgedgeRpaired_nocamera.xml @ 82:b21cd7bec41f draft

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author fubar
date Wed, 26 Feb 2014 21:49:45 -0500
parents f86cb6b724ee
children 3bdf17623d87
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--- a/rgedgeRpaired_nocamera.xml	Wed Feb 26 01:50:06 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Wed Feb 26 21:49:45 2014 -0500
@@ -758,9 +758,10 @@
          DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
          DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
          }
-      norm.factor = calcNormFactors(DGEList)
+      calcNormFactors(DGEList) # -> object$samples$norm.factors
+      ls = colSums(DGEList$counts) * DGEList$samples$norm.factors
       pdf("VOOM_mean_variance_plot.pdf")
-      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
+      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls)
       dev.off()
       # Use limma to fit data
       fit = lmFit(dat.voomed, mydesign)