> HrpDesign
         condition    libType
MeanhrpX   treated single-end
MeanWT   untreated single-end
> conds <- HrpDesign$condition
> conds
[1] treated   untreated
Levels: treated untreated
> library( "DESeq" )
> cds <- newCountDataSet( HrpCountTable, conds )
> head( counts(cds) )
               MeanhrpX MeanWT
TCONS_00000001      236      0
TCONS_00000002      201      0
TCONS_00000003      165      0
TCONS_00000004      152      0
TCONS_00000005       91      0
TCONS_00000006       94      0
> cds <- estimateSizeFactors( cds )
> sizeFactors( cds )
 MeanhrpX    MeanWT 
1.8048037 0.5540769 
> head( counts( cds, normalized=TRUE ) )
                MeanhrpX MeanWT
TCONS_00000001 130.76214      0
TCONS_00000002 111.36945      0
TCONS_00000003  91.42269      0
TCONS_00000004  84.21969      0
TCONS_00000005  50.42100      0
TCONS_00000006  52.08323      0
> cds <- estimateDispersions( cds )
Error in rowSums(sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]),  : 
  'x' must be an array of at least two dimensions