diff rgedgeRpaired_nocamera.xml @ 81:f86cb6b724ee draft

Uploaded

--- a/rgedgeRpaired_nocamera.xml	Wed Feb 26 01:43:53 2014 -0500
+++ b/rgedgeRpaired_nocamera.xml	Wed Feb 26 01:50:06 2014 -0500
@@ -53,7 +53,7 @@
           <param name="edgeR_priordf" type="integer" value="10" size="3" 
            label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n  and prior.df = prior.n * residual.df"
            help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
-          <param name="edgeR_robust" type="select" value="20" size="3" 
+          <param name="edgeR_robust_method" type="select" value="20" size="3" 
            label="Use robust dispersion method"
            help="Use ordinary, anscombe or deviance robust deviance estimates">
              <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
@@ -520,7 +520,7 @@
         filterquantile=0.2, subjects=c(),mydesign=NULL,
         doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
         histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
-        doCook=F,DESeq_fitType="parameteric",robustmeth='ordinary') 
+        doCook=F,DESeq_fitType="parameteric",robust_meth='ordinary') 
 {
   # Error handling
   if (length(unique(group))!=2){
@@ -839,7 +839,7 @@
 #if $edgeR.doedgeR == "T":
   out_edgeR = "$out_edgeR"
   edgeR_priordf = $edgeR.edgeR_priordf  
-  edgeR_robust_meth = "$edgeR.edgeR_robust"
+  edgeR_robust_meth = "$edgeR.edgeR_robust_method"
 #end if
 
 
@@ -897,7 +897,7 @@
                  fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
                  myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
                  doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
-                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robustmeth=edgeR_robust_meth)
+                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robust_meth=edgeR_robust_meth)
 sessionInfo()
 ]]>
 </configfile>