Mercurial > repos > fubar > differential_count_models

diff rgedgeRpaired_nocamera.xml @ 83:3bdf17623d87 draft

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author fubar
date Wed, 26 Feb 2014 23:22:32 -0500
parents b21cd7bec41f
children 2592d79c0f6b
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--- a/rgedgeRpaired_nocamera.xml	Wed Feb 26 21:49:45 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Wed Feb 26 23:22:32 2014 -0500
@@ -758,8 +758,8 @@
          DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
          DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
          }
-      calcNormFactors(DGEList) # -> object$samples$norm.factors
-      ls = colSums(DGEList$counts) * DGEList$samples$norm.factors
+      calcNormFactors(DGEList) 
+      ls = colSums(DGEList\$counts) * DGEList\$samples\$norm.factors
       pdf("VOOM_mean_variance_plot.pdf")
       dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls)
       dev.off()