# HG changeset patch
# User bgruening
# Date 1417021574 18000
# Node ID bac4ebab1122536603dd6ae67557771dd28baa44
# Parent  2f52c1a27205e026b099c8914a58290020c9c771
Uploaded

diff -r 2f52c1a27205 -r bac4ebab1122 deseq2.R
--- a/deseq2.R	Wed Nov 26 11:14:42 2014 -0500
+++ b/deseq2.R	Wed Nov 26 12:06:14 2014 -0500
@@ -49,7 +49,6 @@
 
     select <- order(rowMeans(counts(dds,normalized=TRUE)),decreasing=TRUE)[1:30]
     hmcol <- colorRampPalette(brewer.pal(9, "GnBu"))(100)
-
     rld <- rlogTransformation(dds, blind=TRUE)
     vsd <- varianceStabilizingTransformation(dds, blind=TRUE)
     distsRL <- dist(t(assay(rld)))
@@ -63,6 +62,7 @@
 
 sampleTable<-data.frame()
 factorNames<-c()
+primaryfactor = TRUE
 for(factor in factorsList){
     factorName<-factor[[1]]
     factorNames<-append(factorNames, factorName)
@@ -70,14 +70,19 @@
     c = length(factorValuesMapList)
     for (factorValuesMap in factorValuesMapList){
         for(files in factorValuesMap){
+            fvc = 0
             for(file in files){
-                sampleTable[basename(file),"sampleName"]<-file
+                fvc = fvc+1
+                if(primaryfactor) {
+                    sampleTable[basename(file),"sampleName"]<-paste(fvc,names(factorValuesMap),sep="_")
+                }
                 sampleTable[basename(file),"fileName"]<-file
                 sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_")
             }
         }
         c = c-1
     }
+    primaryfactor = FALSE
 }
 
 factorNames<-rev(factorNames)