Mercurial > repos > fubar > differential_count_models

comparison 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
comparison
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81:f86cb6b724ee 82:b21cd7bec41f
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 norm.factor = calcNormFactors(DGEList) 761 calcNormFactors(DGEList) # -> object$samples$norm.factors
762 ls = colSums(DGEList$counts) * DGEList$samples$norm.factors
762 pdf("VOOM_mean_variance_plot.pdf") 763 pdf("VOOM_mean_variance_plot.pdf")
763 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor) 764 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = ls)
764 dev.off() 765 dev.off()
765 # Use limma to fit data 766 # Use limma to fit data
766 fit = lmFit(dat.voomed, mydesign) 767 fit = lmFit(dat.voomed, mydesign)
767 fit = eBayes(fit) 768 fit = eBayes(fit)
768 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none") 769 rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")