Mercurial > repos > fubar > differential_count_models

comparison 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
comparison
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82:b21cd7bec41f 83:3bdf17623d87
756 DGEList = DGEList(counts=workCM, group = group) 756 DGEList = DGEList(counts=workCM, group = group)
757 DGEList = estimateGLMCommonDisp(DGEList,mydesign) 757 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
758 DGEList = estimateGLMTrendedDisp(DGEList,mydesign) 758 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
759 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) 759 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
760 } 760 }
761 calcNormFactors(DGEList) # -> object$samples$norm.factors 761 calcNormFactors(DGEList)
762 ls = colSums(DGEList$counts) * DGEList$samples$norm.factors 762 ls = colSums(DGEList\$counts) * DGEList\$samples\$norm.factors
763 pdf("VOOM_mean_variance_plot.pdf") 763 pdf("VOOM_mean_variance_plot.pdf")
764 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls) 764 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls)
765 dev.off() 765 dev.off()
766 # Use limma to fit data 766 # Use limma to fit data
767 fit = lmFit(dat.voomed, mydesign) 767 fit = lmFit(dat.voomed, mydesign)