Dear list, I am using an ExpressionSet and generating figures using subsets of genes via boxplot (oligo) and plotlines (limma). > class(zf.rma.sub1) [1] "ExpressionSet" attr(,"package") [1] "Biobase" My data in the expression set is log2-transformed, as expected: > exprs(zf.rma)[1:3,1:2] 220302_4-24-08_1cell_0004_532.xys 220302_4-24-08_1cell_0004_635.xys AA494792 14.730366 14.623973 AA494800 14.314152 13.728564 AA494831 6.960698 6.748818 My lineplots also look fine, but for some reason the y-axis on my boxplots automatically converts to log10 and I can only fix it by doing something stupid and clunky like this after I call the boxplot: axis(2, at=c(3.0,3.2,3.4,3.6,3.8,4.0), lab=c("6","8","10","12","14","16")) which isn't actually precise anway. Any ideas? Many thanks, Farhad Imam -------------------------------------------------- Farhad Imam, MD, PhD Postdoctoral Fellow, Schier Lab Department of Molecular and Cellular Biology Harvard University (617) 496-4910 fimam@mcb.harvard.edu [[alternative HTML version deleted]]

Hi Farhad, I'll upload a fix very soon. Thank you for the report. b On Aug 19, 2009, at 1:24 PM, Farhad Imam wrote: > Dear list, > > I am using an ExpressionSet and generating figures using subsets of > genes via boxplot (oligo) and plotlines (limma). > >> class(zf.rma.sub1) > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" > > My data in the expression set is log2-transformed, as expected: > >> exprs(zf.rma)[1:3,1:2] > 220302_4-24-08_1cell_0004_532.xys > 220302_4-24-08_1cell_0004_635.xys > AA494792 14.730366 > 14.623973 > AA494800 14.314152 > 13.728564 > AA494831 6.960698 > 6.748818 > > My lineplots also look fine, but for some reason the y-axis on my > boxplots automatically converts to log10 and I can only fix it by > doing something stupid and clunky like this after I call the boxplot: > > axis(2, at=c(3.0,3.2,3.4,3.6,3.8,4.0), > lab=c("6","8","10","12","14","16")) > > which isn't actually precise anway. Any ideas? > > Many thanks, > > Farhad Imam > > -------------------------------------------------- > Farhad Imam, MD, PhD > Postdoctoral Fellow, Schier Lab > Department of Molecular and Cellular Biology > Harvard University > > (617) 496-4910 > fimam at mcb.harvard.edu > > [[alternative HTML version deleted]] > > _______________________________________________ > 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