Hello Everyone, I have encountered an unexpected behaviour in limma vennDiagram function and I am unsure whether that is the intended behaviour and if so, what the interpretation is. Here are the versions I am using: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.6.6 loaded via a namespace (and not attached): [1] tools_2.12.0 I have analysed my data using limma and then I got whether the related t-statistics are up, down or not significant for three contrasts of interest: results <- decideTests(fit2, method = "separate", adjust.method = "none", p.value = 0.01) and then I generated a vennDiagram: ## First diagram vennDiagram(results[,c(1,3,5)],include=c("up","down"),counts.col=c("re d","green")) ### this produces the attached image 1 showing no intersection between Comp3 and Comp5. However, vennCounts gives a different story: vennCounts(results[,c(1,3,5)]) Comp1 Comp3 Comp5 Counts [1,] 0 0 0 17366 [2,] 0 0 1 305 [3,] 0 1 0 141 [4,] 0 1 1 128 [5,] 1 0 0 156 [6,] 1 0 1 40 [7,] 1 1 0 25 [8,] 1 1 1 2 vennDiagram(vennCounts(results[,c(1,3,5)])) ### this produce the attached image 2 So, image1 shows no intersection between Comp3 and Comp5, but image2 shows an intersection between Comp3 and Comp5. My question is shouldn't the numbers agree between both venn diagrams? Thank you for your clarifications! Lourdes

Hi Lourdes, On 2/17/2011 9:40 PM, Lourdes Pe?a Castillo wrote: > Hello Everyone, > > I have encountered an unexpected behaviour in limma vennDiagram function and > I am unsure whether that is the intended behaviour and if so, what the > interpretation is. > > Here are the versions I am using: >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_3.6.6 > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > > I have analysed my data using limma and then I got whether the related > t-statistics are up, down or not significant for three contrasts of > interest: > > results<- decideTests(fit2, method = "separate", adjust.method = "none", > p.value = 0.01) > > and then I generated a vennDiagram: > > ## First diagram > vennDiagram(results[,c(1,3,5)],include=c("up","down"),counts.col=c(" red","green")) > ### this produces the attached image 1 showing no intersection between Comp3 > and Comp5. > > However, vennCounts gives a different story: > > vennCounts(results[,c(1,3,5)]) > Comp1 Comp3 Comp5 Counts > [1,] 0 0 0 17366 > [2,] 0 0 1 305 > [3,] 0 1 0 141 > [4,] 0 1 1 128 > [5,] 1 0 0 156 > [6,] 1 0 1 40 > [7,] 1 1 0 25 > [8,] 1 1 1 2 > > vennDiagram(vennCounts(results[,c(1,3,5)])) ### this produce the attached > image 2 > > So, image1 shows no intersection between Comp3 and Comp5, but image2 shows > an intersection between Comp3 and Comp5. > > My question is shouldn't the numbers agree between both venn diagrams? Not necessarily (and not likely, really). The first diagram shows only those genes that were either up in both samples or down in both samples. The second diagram also includes genes that were up in one sample and down in the other, which is a less restrictive criterion. Best, Jim > > Thank you for your clarifications! > > Lourdes > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues