Hello,

I have a simple experiment.

3 biological replicates with the same treatment.

I perform the analysis with Robin, and at when i look to the venn diagrams, up, down and differenciated genes they have the same numbers the total of spots of the array.

Can you say where is the problem? Off cours differences must be seen...

Thank you

Eva Oliveira

Hi Eva,

that indeed should probably not happen. Could you maybe post the three
Venn diagrams that Robin (btw: which version were you using) generated
so i can have a look?

A Venn diagram of the experiment you describe (assuming i understand you
correctly and you have 3 replicates of a treatment and 3 replicates of a control
condition) would just show one circle in the middle with the number of significantly
regulated genes in the middle and the number of not regulated genes in the lower
right corner. In a situation where none of the genes were called significantly changed,
you would see a 0 in the middle of all three Venn diagrams and the total number of genes
on the array in the lower right corner... if your plots look like this you might
want to try and relax the p-value threshold a bit.

I hope that helps,
cheers,
Marc

Thanks for your answer.
Right now everything is OK!

Hi Eva,

I am happy to hear that everything is alright now. It would be great if
you could quickly explain how the problem was resolved - or was it
just a misunderstanding of the Venn diagrams? In that case it would
also be important to know because it would mean i need to make the
explanation of Venn diagrams in the manual better understandable.

Thanks for your feed back,
Marc

Hii,

I notice that there are any problem at all. What happen is that the changes on the genes are not statistically different, so the venn diagrams show 0 genes for each category.

Thank you!!

Hi Eva,

i see - thanks again for your feed back.

cheers,
Marc