GO annotation VENN Diagram

[cement_head]

Hi,

I have two data sets (transcriptomes) that have been GO annotated. For one of the sets, I ONLY have the GO ID's.

This is my question: Can I compare/contrast these two datasets based on their GO ID's alone and then somehow draw a VENN Diagram?

If so, please recommend a program/procedure/paper that outlines this task.

Thanks,
Andor

[mgogol]

Yes. Paste the lists of ids in here?

http://bioinfogp.cnb.csic.es/tools/venny/

[cement_head]

...or I can use the diff command (Linux) to generate the files

[mgogol]

There's lots of ways to draw venn diagrams in R if you're looking for something more programmatic...

[cement_head]

There's lots of ways to draw venn diagrams in R if you're looking for something more programmatic...

Ok, so I've installed R (Ubuntu 12.04). Is there a good GUI for a beginner & how do I install the GUI for R?

Also, how do I install the "venneuler" module?

Thanks,
Andor

[GenoMax]

Ok, so I've installed R (Ubuntu 12.04). Is there a good GUI for a beginner & how do I install the GUI for R?

Thanks,
Andor

http://stats.stackexchange.com/quest...ogramming-in-r

[mgogol]

install.packages("venneuler") might work? Or download from cran and install.

I've had luck also with Vennerable. Limma also has a venn drawing function "vennDiagram". There's also library(VennDiagram).

[mgogol]

This is a bit outdated, but there's a presentation I did for R user group on venn diagrams using library(VennDiagram)

https://drive.google.com/folderview?id=0B50vcj1ewWESZHNfdXVQNVRLTFE&usp=sharing

There's some code and data there. Not the simplest, but it's a starting point...