[BioC] Venn Diagrams in Limma

Gordon Smyth smyth at wehi.edu.au
Tue Oct 28 13:41:27 MET 2003

At 10:23 PM 28/10/2003, Jason Skelton wrote:
>Gordon Smyth wrote:
>>Venn diagrams are by their nature simply overall counts. But you can 
>>easily identify the relevant genes from the 'classification' object from 
>>which the Venn diagram is computed.
>Not sure how this is done, the object I have created in ClassifyTests has 
>classification (0 and 1's) and Fstats associated with it
>am I looking in the wrong place ?  I have a list of genes made from 
>uniquegenelist is this the list I'm wanting to access ?
>My VennCounts object is:
>     DIF1 DIF2 DIF3 Counts
>[1,]    0    0    0   1925
>[2,]    0    0    1     18
>[3,]    0    1    0     26
>[4,]    0    1    1      5
>[5,]    1    0    0     70
>[6,]    1    0    1     13
>[7,]    1    1    0     90
>[8,]    1    1    1     59
>[1] "VennCounts"
>could you give an example of how to associate each of the 8 counts with 
>genes from the uniquegenelist (OR other)

Go one step back, to the classification matrix which comes out of 
classifyTests(). That gives you a classification matrix with one row for 
each gene in the uniquegenelist.

>>I'd also like to be able to use the false discovery rate option that can 
>>beused in classifyTestsP method for my venn diagram but I also want to 
>>use data that I've received from makeContrasts and contrast.fit which I 
>>can only use in classifyTests but I can't use "fdr" in that function....
>>Is there a particular reason why I can't do this ?
>Yes there is. classifyTests() uses a method intended to control false 
>discovery rate across contrasts. This is not compatible with the simple 
>p.adjust() approach to controling FDR across genes. I suggest that you 
>simply find what unadjusted p-value corresponds to your desired FDR level 
>and enter that to classifyTests().
>OK that makes more sense now thanks.
>I have yet more questions about the heatdiagram option
>My gene names are very long 28+ characters long is there a heatdiagram 
>specific command that alters the size of the box that the heatmap covers ?
>So that genes appearing on the plot are not truncated (I've tried some of 
>the R commands for Margins etc but they don't want to work with high level 

No there isn't. imageplot truncates names to 15 characters. You would have 
to modify the code yourself to change that.

>Also in the heatdiagram you can specify EB$t and fit$coef
>e.g. heatdiagram(newDIF123SEPcontrastfitEB$t, 
>newDIF123SEPcontrastsfit$coef etc)
>you can specify the critical.primary argument  which  is the critical 
>value "above" which genes are considered significant.
>If you want to use EB$p.value fit$coef
>e.g. heatdiagram(newDIF123SEPcontrastfitEB$p.value, 
>newDIF123SEPcontrastsfit$coef etc)
>you can't specify the critical.primary because you need to specify a 
>maximum value e.g(0.05) rather than minimum as your cutoff

Use heatDiagram() instead. That function will accept a classification 
matrix from classifyTestsP which will allow you to specify your desired 
p-value cutoff.


>Thanks for you help

More information about the Bioconductor mailing list