[BioC] odd results from vennCounts()

Gordon Smyth smyth at wehi.edu.au
Thu Sep 2 12:52:18 CEST 2004


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



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