Hi Jenny. You won't be able to estimate the negative binomial dispersion parameter without replication. In edgeR, you can set doPoisson=TRUE in deDGE() which basically just sets that parameter to 0. I think this comes out quite similar to sage.test(). Cheers, Mark On 24/07/2009, at 5:41 AM, Naomi Altman wrote: > I used sage.test for NGS libraries. Worked fine. > --Naomi > > At 12:02 PM 7/23/2009, Jenny Drnevich wrote: >> Forgot to Cc: BioC the first time... >> >>> Date: Thu, 23 Jul 2009 10:23:11 -0500 >>> To: "Mark Robinson" <mrobinson at="" wehi.edu.au=""> >>> From: Jenny Drnevich <drnevich at="" illinois.edu=""> >>> Subject: edgeR with only 1 replicate? >>> >>> Hi Mark and others, >>> >>> Can edgeR be used if you only have 1 replicate per group? If not, >>> do you or anyone know of the best way to analyze frequencies of >>> Illumina's DGE tags. I'm thinking Fisher's exact test or Z-test, >>> but it would be nice if the functions for sequencing data were >>> already written. I see from searching the BioC archives that there >>> is sage.test, which is Fisher's exact test - anything else? Most >>> of the work done on this has been in the context of SAGE >>> libraries, and I wonder if it scales properly to NGS libraries. >>> >>> Thanks, >>> Jenny >>> >>> Jenny Drnevich, Ph.D. >>> >>> Functional Genomics Bioinformatics Specialist >>> W.M. Keck Center for Comparative and Functional Genomics >>> Roy J. Carver Biotechnology Center >>> University of Illinois, Urbana-Champaign >>> >>> 330 ERML >>> 1201 W. Gregory Dr. >>> Urbana, IL 61801 >>> USA >>> >>> ph: 217-244-7355 >>> fax: 217-265-5066 >>> e-mail: drnevich at illinois.edu >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 > (Statistics) > University Park, PA 16802-2111 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852