Possible inconsistency between Venn plot and UpSetR plots

[tamuanand]

Hi

I somehow find some inconsistency with the VennList plot and the UpSetR plot as shown in image below

My list1 file has 2176 genes and the UpDown list from ideal is 2065 genes

• on the Venn Plot - the sum of the genes is correct for the UpDown list, but I think it is wrong for the sum of the genes from list1
• on the UpSetR plot - the sum of the genes is incorrect for UpDown (1705 + 242 = 1947) and is also wrong for list1 (1705 + 358 = 2063)

Am I misinterpreting something?

[tamuanand]

Hi @federicomarini

Using airway demo dataset, I could reproduce the Venn-UpSet inconsistency on http://shiny.imbei.uni-mainz.de:3838/ideal/

Important info for reproducing:

Data Setup Tab -- use Dex for Design
Counts Overview Tab - filter dds using row means >10    (the dds object will now be 15998 genes - 8 samples)
Extract results - trt vs untrt  (there will be 2705 DE genes - out of 15998)
Functional Analysis tab - use the attached file "322_List_1.txt" for list1 

Look at the Venn and UpSet plots

Also attached the ideal html report within the zip file - this is for reproducing this analysis and also underscores/endorses what ideal is for - interactive yet reproducible analysis

ideal_GH_issue_Venn_vs_Upset_Inconsistency.zip

322_List_1.txt

[federicomarini]

I admit it is quite strange, but one possible thought is this: maybe some genes have a gene name which is common across gene id - and somehow this is handled in different ways by the venn diagram function (gplots::venn) and the UpSet plot? I will revisit this soon, thanks for pointing the attention to this aspect!