Question: Fwd: edgeR with only 1 replicate?
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gravatar for Jenny Drnevich
10.0 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k 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
sequencing sage edger • 406 views
ADD COMMENTlink modified 10.0 years ago by Naomi Altman6.0k • written 10.0 years ago by Jenny Drnevich1.9k
Answer: Fwd: edgeR with only 1 replicate?
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gravatar for Naomi Altman
10.0 years ago by
Naomi Altman6.0k
Naomi Altman6.0k 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
ADD COMMENTlink written 10.0 years ago by Naomi Altman6.0k
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
ADD REPLYlink written 10.0 years ago by Mark Robinson1.1k
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