[BioC] Differential expression without replicates

Mark Robinson mark.robinson at imls.uzh.ch
Tue Aug 28 09:07:08 CEST 2012

Hi Srikanth,

No replicates is not an ideal situation.

In the user manual, edgeR has a section "What to do if you have no replicates":

Similarly, DESeq has a section "Working without any replicates":

Did you try these?

Best regards,

On 28.08.2012, at 08:51, Srinivas M. Srikanth wrote:

> HI all,
> I have paired-end RNAdata from five different tissues of the same organism,
> I calculated the read counts using HTSeq tools and now I want to see which
> are the transcripts which are differentially expressed (if any) among the
> five tissues (I do not have any replicates). I have tried using edgeR and
> DESeq packages but not getting even a single value to be significant. Can
> anyone suggest the possibilities??
> Regards,
> Srikanth
> -- 
> Srinivas M. Srikanth
> Ph.D. Student
> Institute of Bioinformatics
> Discoverer, 7th Floor,
> International Technology Park,
> Bangalore, India
> Mob:+919019114878
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Prof. Dr. Mark Robinson
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University of Zurich
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