Question

VennDiagram from two TestResults matrices

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shania90.lk ▴ 10

@shania90lk-9656

Last seen 7.9 years ago

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 • 1.2k views

ADD COMMENT • link updated 7.9 years ago by Gordon Smyth 50k • written 7.9 years ago by shania90.lk ▴ 10

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

ADD REPLY • link 7.9 years ago Aaron Lun ★ 28k

score 1 · Answer 1 · 2016-05-25

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Gordon Smyth 50k

@gordon-smyth

Last seen 10 hours ago

WEHI, Melbourne, Australia

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

ADD COMMENT • link 7.9 years ago Gordon Smyth 50k

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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 REPLY • link 7.9 years ago shania90.lk ▴ 10