Hello everyone, I have been getting some stange results from vennCounts() package limma, without any assocaited warnings. example: try <- matrix(9,nrow=10,ncol=3) try[10,3] <- 0.2 try[1,2] <- 0.2 m <- classifyTestsF(try) a <- vennCounts(m) # vennDiagram(a) If i've understood correctly,it seems that this occurs when one of the groups is all 1's / all "up". If you add in try[2,1] <- 0.2 to the above code ie. break the homogeneity of that "all 1" group, it seems to give sensible results again. Am i making some kind of mistake to get these odd results or should the function be printing some kind of warning about a homogenous group, so that i know not to trust the results? Thanks for your help, Jacqueline [[alternative HTML version deleted]]

At 07:33 PM 2/09/2004, Jacqueline Hall wrote: >Hello everyone, > >I have been getting some stange results from vennCounts() package limma, >without any assocaited warnings. > >example: > >try <- matrix(9,nrow=10,ncol=3) >try[10,3] <- 0.2 >try[1,2] <- 0.2 >m <- classifyTestsF(try) >a <- vennCounts(m) ># vennDiagram(a) What do you think is strange? When I run it, the venn diagram seems a perfectly sensible reflection of the data you gave it. You gave it all large numbers (9 is pretty large for a std normal) except for two values, so it classified all the large values as significant and the two low values as non-significant. What else could you expect it to do? Gordon >If i've understood correctly,it seems that this occurs when one of the >groups is all 1's / all "up". >If you add in try[2,1] <- 0.2 to the above code ie. break the homogeneity of >that "all 1" group, it seems to give sensible results again. >Am i making some kind of mistake to get these odd results or should the >function be printing some kind of warning about a homogenous group, so that >i know not to trust the results? > >Thanks for your help, > >Jacqueline

I have to back-track a bit on my previous reply. There is a bug in vennCounts() in the BioC Release 1.3 version of limma which does affect this example. The bug was fixed about 3 months ago. It affected limma versions 1.5.2 to 1.6.11. Please upgrade your copy of limma from http://bioinf.wehi.edu.au/limma Gordon At 07:33 PM 2/09/2004, Jacqueline Hall wrote: >Hello everyone, > >I have been getting some stange results from vennCounts() package limma, >without any assocaited warnings. > >example: > >try <- matrix(9,nrow=10,ncol=3) >try[10,3] <- 0.2 >try[1,2] <- 0.2 >m <- classifyTestsF(try) >a <- vennCounts(m) ># vennDiagram(a) > >If i've understood correctly,it seems that this occurs when one of the >groups is all 1's / all "up". >If you add in try[2,1] <- 0.2 to the above code ie. break the homogeneity of >that "all 1" group, it seems to give sensible results again. >Am i making some kind of mistake to get these odd results or should the >function be printing some kind of warning about a homogenous group, so that >i know not to trust the results? > >Thanks for your help, > >Jacqueline