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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!

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  • $\begingroup$ Can you be a bit more specific? The vast majority of genes will probably be similar, what question do you want to answer? $\endgroup$
    – user3051
    Oct 8, 2020 at 19:45
  • $\begingroup$ Genes "that are expressed the same" would be "the genes that are NOT differentially expressed" so if you cannot study the latter you cannot study the former. $\endgroup$
    – haci
    Oct 8, 2020 at 19:57
  • $\begingroup$ Please edit your question and give us some details. Do you already have expression data? What data do you have? What kind of format are they in? Why would you look at all genes that are similarly expressed in all samples? That won't help you identify genes related to a phenotype, not without a control. $\endgroup$
    – terdon on strike ♦
    Oct 9, 2020 at 12:38
  • $\begingroup$ standard deviation/mean? $\endgroup$
    – Greg
    Oct 9, 2020 at 16:37
  • $\begingroup$ I have edit the question, I hope now is more clear. thanks! $\endgroup$
    – Mee
    Oct 12, 2020 at 14:57

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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.

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