Question: Creating a Venn Diagram from Microarray Data
0
gravatar for briannawalters97
3.3 years ago by
United States
briannawalters970 wrote:

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

ADD COMMENTlink modified 3.3 years ago by mkulecka300 • written 3.3 years ago by briannawalters970

What do you mean by similar genes?

ADD REPLYlink written 3.3 years ago by pld4.8k
2
gravatar for TriS
3.3 years ago by
TriS3.6k
United States, Buffalo
TriS3.6k wrote:

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 tools 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

ADD COMMENTlink written 3.3 years ago by TriS3.6k

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

ADD REPLYlink written 3.3 years ago by Daniel Swan13k

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

ADD REPLYlink written 3.3 years ago by briannawalters970

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

ADD REPLYlink written 3.3 years ago by TriS3.6k

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?

ADD REPLYlink written 3.3 years ago by briannawalters970

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

ADD REPLYlink written 3.3 years ago by pld4.8k
0
gravatar for mkulecka
3.3 years ago by
mkulecka300
European Union
mkulecka300 wrote:

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. 

ADD COMMENTlink written 3.3 years ago by mkulecka300
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