Looking for genes that are expressed the same in all the samples I have 5 samples (from a RNA seq experiment) from patients but I have no control, so since we can't look for the differentially expressed genes we want to look for the genes that have similar expression in all the sample.
We want to do that to see if some genes that can be involved are among those expressed in all the samples.
I have never done that, I do not know how to do it and I cant find any info about it, so any ideas are welcome.
Thanks!
I cannot think of a way without performing differential expression analysis. Since you don't have controls, what you could do is assigning some of the samples as controls.
Let's say you have samples A, B, C, D, E and F. You can perform differential expression analysis A, B, C (i.e. treatment) versus D, E (control). If you perform this for all possible combinations (that would be 5 choose 2 which is equal to 5 choose 3 if you decide to go for 3 vs 2 splits) and filter for genes which do not show up in any DE list you end up with the genes that are expressed similarly in al of these samples.