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? Thanks for your attention. Best regards, -- Liliane Santana Bacharel em Ciência da Computação - UFS Mestranda em Ciência da Computação - USP Bioinformata - IIEP Albert Einstein [[alternative HTML version deleted]]

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 changes. Best, Jim > > Thanks for your attention. > > Best regards, > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099