# HG changeset patch
# User fubar
# Date 1393397033 18000
# Node ID 335abf087bc558457d2a6ffbbe76c8666d13a783
# Parent  17d82de7a2d9ce6d57b5553fe3a8545073d8f0cb
Uploaded

diff -r 17d82de7a2d9 -r 335abf087bc5 rgedgeRpaired_nocamera.xml
--- a/rgedgeRpaired_nocamera.xml	Wed Feb 26 00:23:05 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Wed Feb 26 01:43:53 2014 -0500
@@ -594,7 +594,7 @@
   print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
   print.noquote('Using design matrix:')
   print.noquote(mydesign)
-  if (doedgeR) {
+  if (doedgeR == T) {
   sink('edgeR.log')
   #### Setup DGEList object
   DGEList = DGEList(counts=workCM, group = group)
@@ -608,9 +608,10 @@
        estpriorn = getPriorN(DGEList)
        print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
      } else { 
-       DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth) 
+       DGEList = estimateGLMRobustDisp(DGEList,design=mydesign, prior.df = edgeR_priordf, maxit = 6, residual.type = robust_meth)
           }
-  }
+    
+  
   DGLM = glmFit(DGEList,design=mydesign)
   DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
   efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
@@ -818,7 +819,7 @@
 out_DESeq2 = F
 out_VOOM = "$out_VOOM"
 edgeR_robust_meth = "ordinary" # control robust deviance options
-doDESeq2 = F
+doDESeq2 = $DESeq2.doDESeq2
 doVoom = $doVoom
 doCamera = F
 doedgeR = $edgeR.doedgeR