Dear Ingunn There are a number of interesting papers on reproducibility of NGS results. 't Hoen, PA, Ariyurek, Y, Thygesen, HH, Vreugdenhil, E, Vossen, RH, de Menezes, RX, Boer, JM, van Ommen, GJ & den Dunnen, JT 2008, 'Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms', Nucleic Acids Research, vol. 36, no. 21, p. e141. Marioni, JC, Mason, CE, Mane, SM, Stephens, M & Gilad, Y 2008, 'RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays', Genome Res, vol. 18, no. 9, pp. 1509-17. Bullard, JH, Purdom, EA, Hansen, KD, Durinck, S & Dudoit, S 2009, 'Statistical Inference in mRNA-Seq: Exploratory Data Analysis and Differential Expression', U.C. Berkeley, 247. Naomi At 03:16 AM 2/1/2010, you wrote: >Dear Dr. Altman > >I send this off the bioconductor mail list as it >is more of a NGS question than an R question. >I am curious about how the reproducibility >between biological replicates usually is. I send >this question to you since you answered the more >technical question about how to measure it, you >may have some experience about it. I am not >currently involved in any projects on NGS, but >want to keep updated and this question is very >relevant for planning experiments. I hope for an informative reply. > >Best regards > >Ingunn Berget (Dr. Scient) >UMB, box 5003, IHA >1432 Ås >Norway > >Centre for Integrative Genetics, www.cigene.no >Centre for Biospectroscopy and Data Modelling, www.specmod.org > >-----Original Message----- > >From: bioconductor-bounces@stat.math.ethz.ch > [<mailto:bioconductor->mailto:bioconductor- > >bounces@stat.math.ethz.ch] On Behalf Of Naomi Altman > >Sent: Saturday, January 30, 2010 4:10 AM > >To: Pete Shepard; bioconductor@stat.math.ethz.ch; bioc-sig- sequencing- > >request@r-project.org > >Subject: Re: [BioC] reproducibility between reads? > > > >cor(log(count.sample1+.25),log(count.sample2+.25)) works pretty well. > > > >--Naomi > > > >At 05:57 PM 1/29/2010, Pete Shepard wrote: > >>Dear List, > >> > >>I am attempting to measure the reproducibility of two biological > >replicate > >>RNA seq Solexa reads. Are there any Bioconductor packages that can > >handle > >>this? > >> > >>TIA > >> > >> [[alternative HTML version deleted]] > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor@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@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 [[alternative HTML version deleted]]