Mercurial > repos > fubar > differential_count_models

comparison rgedgeR/rgedgeRpaired.xml @ 11:e7733b353702 draft

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author fubar
date Sat, 27 Jul 2013 01:43:13 -0400
parents 755cf582f2c4
children aa528c834664
comparison
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10:755cf582f2c4 11:e7733b353702
605 if (doedgeR == F) { 605 if (doedgeR == F) {
606 #### Setup DGEList object 606 #### Setup DGEList object
607 DGEList = DGEList(counts=workCM, group = group) 607 DGEList = DGEList(counts=workCM, group = group)
608 DGEList = calcNormFactors(DGEList) 608 DGEList = calcNormFactors(DGEList)
609 DGEList = estimateGLMCommonDisp(DGEList,mydesign) 609 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
610 comdisp = DGEList\$common.dispersion
611 DGEList = estimateGLMTrendedDisp(DGEList,mydesign) 610 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
612 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign) 611 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
612 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
613 norm.factor = DGEList\$samples\$norm.factors
613 } 614 }
614 pdf("VOOM_mean_variance_plot.pdf") 615 pdf("VOOM_mean_variance_plot.pdf")
615 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor) 616 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
616 dev.off() 617 dev.off()
617 # Use limma to fit data 618 # Use limma to fit data