[BioC] RNA differential expression

James W. MacDonald jmacdon at uw.edu
Wed Oct 16 16:30:17 CEST 2013

Hi Liliane,

On Wednesday, October 16, 2013 9:44:06 AM, Liliane Santana wrote:
> Good morning,
> I work with mirnas analysis and I would like your help (if possible).
> I have two set of tumor samples of human mirnas (N0 and N+, with and
> without metastasis respectively) that were sequenced with SOLiD sequencer
> and I would like to know if I there is a way to analyse differential
> expression with Deseq. I saw that Deseq is usually used to compare paired
> samples (for example, tumor and control of the same patient). I tried to
> apply a example with my tests, using the nbinomTest function, but I didn't
> get results (it returned NA)... Can anybody help me?

What you have told us is not nearly sufficient for anybody to help. 
Instead of saying what you did, show us the code, and the results, 
along with the output you get from sessionInfo().

As an aside, DESeq isn't primarily designed for paired samples. You can 
use any number of experimental designs, including yours (contingent 
upon 'two set of tumor samples' meaning that you have more than one 
sample of each type). If you don't have replication, you won't be able 
to do statistical tests, but may be able to compute things like fold 



> Thanks for your attention.
> Best regards,
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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