Mercurial > repos > fubar > differential_count_models

comparison rgedgeR/rgedgeRpaired.xml @ 10:755cf582f2c4 draft

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author fubar
date Sat, 27 Jul 2013 01:39:29 -0400
parents 2e35432ee040
children e7733b353702
comparison
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9:2e35432ee040 10:755cf582f2c4
600 } 600 }
601 } 601 }
602 602
603 if (doVoom == T) { 603 if (doVoom == T) {
604 sink('VOOM.log') 604 sink('VOOM.log')
605 if (doedgeR == F) {
606 #### Setup DGEList object
607 DGEList = DGEList(counts=workCM, group = group)
608 DGEList = calcNormFactors(DGEList)
609 DGEList = estimateGLMCommonDisp(DGEList,mydesign)
610 comdisp = DGEList\$common.dispersion
611 DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
612 DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
613 }
605 pdf("VOOM_mean_variance_plot.pdf") 614 pdf("VOOM_mean_variance_plot.pdf")
606 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor) 615 dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
607 dev.off() 616 dev.off()
608 # Use limma to fit data 617 # Use limma to fit data
609 fit = lmFit(dat.voomed, mydesign) 618 fit = lmFit(dat.voomed, mydesign)