Question: VennDiagram from two TestResults matrices
0
gravatar for shania90.lk
3.4 years ago by
shania90.lk10
shania90.lk10 wrote:

Hi all,

I would kindly like to know whether it is possible to use two different testResults matrices from the same experiment (e.g. decideTests object from root and shoot) to create a venn diagram using limma vennDiagram() function? I know you might ask why? Because I can easily add the two tissues together and get the final results. However, I would like to analyse the tissues separately to see whether there is an effect of variance by having two tissues together in one statistical model (which would be like comparing a brain to a liver). As the final step of this I would like to see the overlap between the results I got for roots and shoots. Combining the matrices doesn't work because the number of genes are different in each object. I would therefore, kindly like to ask guidance from the experts in the field.

Thank you,

Shani.

limma venn diagram • 505 views
ADD COMMENTlink modified 3.4 years ago by Gordon Smyth38k • written 3.4 years ago by shania90.lk10

Please put down some code describing what you would like to do. It's hard to determine from just a plain-English description.

ADD REPLYlink written 3.4 years ago by Aaron Lun25k
Answer: VennDiagram from two TestResults matrices
1
gravatar for Gordon Smyth
3.4 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

If you have different rows (genes) in the two analyses, then no.

ADD COMMENTlink written 3.4 years ago by Gordon Smyth38k

Thank you for the prompt reply Gordon. I have to find an alternative way then. Maybe create the DGEList for the whole set of samples and apply Voom for separate experimental groups (e.g. subset of root results from the DGEList object and subset of shoot results from the DGEList object, etc.).

ADD REPLYlink written 3.4 years ago by shania90.lk10
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