[BioC] Limma vennDiagram function

[James W. MacDonald]

Hi Lourdes,

On 2/17/2011 9:40 PM, Lourdes Peña 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
>
>
>
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-- 
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
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