Hi, using DESeq2 1.2.10, I am getting slightly different results than with previous version (included in Bioconductor 2.12) using otherwise unchanged parameters. I could not find a changelog for 1.2.10, but I am wondering what the difference of this latest version is w.r.t previous versions. Thanks, Carl -- ------------------------------------------------------------------ C a r l H E R R M A N N ------------------------------------------------------------------ Institut f?r Pharmazie und Molekulare Biotechnologie Universit?t Heidelberg DKFZ Heidelberg - Department of Theoretical Bioinformatics Im Neuenheimer Feld 580 D-69120 Heidelberg tel.: +49 (0) 6221 42-3612 email : c.herrmann at dkfz.de web: http://biologie.univ-mrs.fr/carlherrmann

hi Carl, The changelog is in the NEWS file, this is listed on the package landing page. or from within R you can use: news(Version > 1.0, package="DESeq2") Mike On Mon, Apr 7, 2014 at 3:56 AM, Carl Herrmann <c.herrmann@dkfz- heidelberg.de=""> wrote: > Hi, > > using DESeq2 1.2.10, I am getting slightly different results than with > previous version (included in Bioconductor 2.12) using otherwise unchanged > parameters. > I could not find a changelog for 1.2.10, but I am wondering what the > difference of this latest version is w.r.t previous versions. > > Thanks, > > Carl > > -- > ------------------------------------------------------------------ > C a r l H E R R M A N N > ------------------------------------------------------------------ > Institut für Pharmazie und Molekulare Biotechnologie > Universität Heidelberg > DKFZ Heidelberg - Department of Theoretical Bioinformatics > Im Neuenheimer Feld 580 > D-69120 Heidelberg > tel.: +49 (0) 6221 42-3612 > email : c.herrmann@dkfz.de > web: http://biologie.univ-mrs.fr/carlherrmann > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor [[alternative HTML version deleted]]

http://www.bioconductor.org/packages/release/bioc/news/DESeq2/NEWS On 4/7/2014 3:56 AM, Carl Herrmann wrote: > Hi, > > using DESeq2 1.2.10, I am getting slightly different results than with > previous version (included in Bioconductor 2.12) using otherwise > unchanged parameters. > I could not find a changelog for 1.2.10, but I am wondering what the > difference of this latest version is w.r.t previous versions. > > Thanks, > > Carl > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ah, so you saw a difference in results from 1.2.4 to 1.2.10? I didn't make any changes other than bug fixes, vignette corrections, and adding a message about multiple factor level contrasts. My notes say I fixed a bug regarding Cook's distance when number of samples = number of parameters (no replicates), and I fixed a bug regarding normalization factors and the outlier replacing function. On Mon, Apr 7, 2014 at 3:18 PM, Carl Herrmann <c.herrmann@dkfz- heidelberg.de=""> wrote: > Hi Mike, > > thanks for your answer, I had seen the NEWS file, but the latest version > that is mentionned in there is 1.2.4. What about the later versions ? > > Carl > > > On 07/04/14 20:23, Michael Love wrote: > >> hi Carl, >> >> The changelog is in the NEWS file, this is listed on the package landing >> page. >> >> or from within R you can use: >> >> news(Version > 1.0, package="DESeq2") >> >> Mike >> >> >> >> >> On Mon, Apr 7, 2014 at 3:56 AM, Carl Herrmann < >> c.herrmann@dkfz-heidelberg.de <mailto:c.herrmann@dkfz- heidelberg.de="">> >> wrote: >> >> Hi, >> >> using DESeq2 1.2.10, I am getting slightly different results than >> with previous version (included in Bioconductor 2.12) using >> otherwise unchanged parameters. >> I could not find a changelog for 1.2.10, but I am wondering what >> the difference of this latest version is w.r.t previous versions. >> >> Thanks, >> >> Carl >> >> -- ------------------------------------------------------------ >> ------ >> C a r l H E R R M A N N >> ------------------------------------------------------------------ >> Institut für Pharmazie und Molekulare Biotechnologie >> Universität Heidelberg >> DKFZ Heidelberg - Department of Theoretical Bioinformatics >> Im Neuenheimer Feld 580 >> D-69120 Heidelberg >> tel.: +49 (0) 6221 42-3612 <tel:%2b49%20%280%29%206221%2042-3612> >> email : c.herrmann@dkfz.de <mailto:c.herrmann@dkfz.de> >> >> web: http://biologie.univ-mrs.fr/carlherrmann >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > -- > ------------------------------------------------------------------ > C a r l H E R R M A N N > ------------------------------------------------------------------ > Institut für Pharmazie und Molekulare Biotechnologie > Universität Heidelberg > DKFZ Heidelberg - Department of Theoretical Bioinformatics > Im Neuenheimer Feld 580 > D-69120 Heidelberg > tel.: +49 (0) 6221 42-3612 > email : c.herrmann@dkfz.de > web: http://biologie.univ-mrs.fr/carlherrmann > ------------------------------------------------------------------ > > [[alternative HTML version deleted]]