Creating a Venn Diagram from Microarray Data

Question

[briannawalters97]

Hello

I am trying to create a venn diagram showing the similar genes of my microarray data. I have used Affymetrix's Transcriptome Analysis Console to get the average signal, fold change, and ANOVA p value of my probe sets, but I am unsure how to use this data to make a venn diagram. I have already tried programs like VennPlex and GeneVenn, but they do not seem to be giving me the correct diagram. Any help would be appreciated.

Thank you

[pld]

What do you mean by similar genes?

Answer 1

[TriS]

Are you using gene names? Can you use R? If so, you can use the venn() function in gplots.

Otherwise you can use this very simple online tool from bioinformatics.lu as long as you have max 3 groups

For more than 3 you can use this other tool from the univ. of Pretoria

[User 59]

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

[briannawalters97]

I don't have the gene names, only probe sets.

[TriS]

gene names, probe names, IDs...any of them works...

[briannawalters97]

The problem that I am having is that these programs are comparing all of the values for my three samples instead of just the values in each row, so instead of showing that my samples have 1 gene in common, it is showing that they have around 1200. How do I avoid this?

[pld]

You should also be able to download the annotation file for your array(s) so you can map probesets to gene IDs or names.

Answer 2

[mkulecka]

https://cran.r-project.org/web/packages/VennDiagram/index.html - I also recommend this R package. You can plot up to five groups with it.