#3 R script terminate with error

[Anonymous]

Originally created by: michel.m...@gmail.com

What steps will reproduce the problem?
1.  let allim run with 3 replicates and settings stored in AllimOptions_2Pexpr
2. ./Allim.py --option-file AllimOptions_2Pexpr
3.

What is the expected output? What do you see instead?
expected: 4 folders as described in the manual, the fourth containing the normalized read counts.
seen: fourth folder only containing the adjusted p-values of exons and genes concerning allelic imbalance

What version of the product are you using? On what operating system?

Allim_1.1 on Ubuntu 14.04

Please provide any additional information below.

R script lm-aov-4lines.r.Rout returns an error (i am using [r3].1.1):  

#try1=data.frame(gene_id=as.character(dt$feature.id[idx[1]]),overall_p_value=pvalue,P1_P2=extract[,"P1-P2"][2],P1h_P2h=extract[,"P1h-P2h"][2])
+     #try1=data.frame(gene_id=as.character(dt$feature.id[idx[1]]),overall_p_value=pvalue,P1_P2=extract[,"P1-P2"][2],P1h_P2h=extract[,"P1h-P2h"][2],P1_P1h=extract[,"P1-P1h"][2],P2_P2h=extract[,"P2-P2h"][2],P1_P2h=extract[,"P1-P2h"][2],P2_P1h=extract[,"P2-P1h"][2])
+
+       try1=data.frame(feature_id=as.character(dt$feature.id[idx[1]]),ASE_pvalue=extract[,"P1h-P2h"][2])
+
+
+       #print (try1)
+       data_vector=rbind(data_vector,try1)
+
+
+ }
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
  contrasts can be applied only to factors with 2 or more levels
Calls: aov ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted