[BioC] Limma and vennDiagram

[Francois Pepin]

Hi Ng,

include='both' will mark a gene as differentially expressed or not 
differentially expressed, ignoring the direction. If your categories are 
A, B and C, a gene that is up in A & B and down in C will end up at the 
intersection of the three categories

include=c('up','down') will do two comparisons. The first ('up') marks 
the gene as overexpressed or not (i.e. underexpressed or unchanged). The 
second does the opposite and only counts underexpressed genes.

You will notice that both sets of counts include the total of your 
genes, as they cannot be considered together. The previous example that 
is up in A & B and down in C would end up being in the A&B intersection 
in 'up', and in C only in the 'down'.

Please tell me if this is not clear.

I am unsure which labels you are talking about that you would like to 
move to the left hand side. Unfortunately, the positions for labels are 
hard-coded in this function. One way would be to use fix(vennDiagram) to 
  change them if you want. If you tell me which ones you want exactly, I 
could send you another version with the position changed.

Francois

Ng Stanley wrote:
> Hi,
> 
> Two questions:
> A) I don't understand the difference between include=c("up", "down"), and
> include="both". The numbers for both venn diagram are different.
> B) How to label on the left hand side ?
> 
> Thanks
> Stanley
> 
> 	[[alternative HTML version deleted]]
> 
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