Mercurial > repos > fubar > differential_count_models

comparison rgedgeRpaired_nocamera.xml @ 105:442d906d8682 draft

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author fubar
date Mon, 03 Mar 2014 00:10:30 -0500
parents 7de681a7c511
children c612d67e63c2
comparison
equal deleted inserted replaced
104:39f7ed5b2fc1 105:442d906d8682
1 <tool id="rgDifferentialCount" name="Differential_Count" version="0.24"> 1 <tool id="rgDifferentialCount" name="Differential_Count" version="0.23">
2 <description>models using BioConductor packages</description> 2 <description>models using BioConductor packages</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.14">biocbasics</requirement> 4 <requirement type="package" version="2.14">biocbasics</requirement>
5 <requirement type="package" version="3.0.3">r303</requirement> 5 <requirement type="package" version="3.0.3">r303</requirement>
6 <requirement type="package" version="1.3.18">graphicsmagick</requirement> 6 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
784 784
785 if (doCamera) { 785 if (doCamera) {
786 doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle, 786 doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
787 outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype) 787 outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
788 } 788 }
789 789 counts.dataframe = c()
790 vennmain = 'no venn'
790 if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) { 791 if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
791 if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) { 792 if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
792 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh) 793 vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
793 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, 794 counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts,
794 VOOM_limma = voomcounts, row.names = allgenes) 795 VOOM_limma = voomcounts, row.names = allgenes)