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Rna -Seq cummeRbund plot issues

I'm using the tuxedo protocol for RNA-Seq data analysis the analysis is complete but it seems there are issues im not sure

CuffSet instance with: 4 samples 47983 genes 309126 isoforms 123858 TSS 0 CDS 287898 promoters 743148 splicing 0 relCDS

The CDS shouldn;t be zero isnt it?

Other issues is cummeRbund is not detecting the replicates I have 4 sample like 

'Sample 1 ,Sample 2(replicate), Sample 3,Sample 4(replicate)'

So any suggestion where am I doing or going wrong ?

rna-seq r
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written by 1769mkc 1769mkc

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