Find the genes that are commonly expression between 3 tissue

Question

[jihed.chouaref]

Hi people,

I hope you can help me with my strange question. I have 3 RNA-seq data from 3 different tissues and I would like to find the genes that are expressed in the same manner between those tissues. When I say expressed in the same manner, this means that if they are either expressed or not expressed. I thought about doing a differential gene expression analysis between the 3 tissues (1v1) and then select the genes that are not differentially expressed between the 3 tissues.

But for reasons that I can not explain, this seems not correct to me. So if anyone has experience or suggestions on the best way to proceed with this, I am open for it !

Thanks in advance for your help!

[Carambakaracho]

How do you want to draw a threshold to discriminate between expressed vs. non expressed genes? In case you've settled this, just convert everything to 0 (not expressed) and 1 (expressed) and you'll ba able to do a simple binary comparison. The tricky part is the threshold definition, considering differences in library size, gene length, etc...

for reasons that I can not explain

Generally with many readers this will cause a reaction best described by the "suspicious eyebrow raise" ...