Hi,

   I have a dataset form RNAseq, I have only the ht-seq-counts results. I have 551 patients with cancers that have been sequenced. So I have only one level, one condition. But I have n=551 patients. Can I use Deseq2 to see a differential expression in my patient cohort even if I have no control. Only one level (one condition= cancer) ?

I have use Deseq2 in the past but it was for a study of difference between cell treated against control.

Here I have no control ...

Is Deseq2 is able to do a differential expression within a single condition?

Thank you very much for your help,

Best regards,

Julie Cardin

Research Assistant and student in bioinformatics.

By definition you can't say if something is different when you only have one group! Different between what?

With that number of patients you could presumably divide into different groups based on stage or gender or presence of metasteses or something. But if you only have one group, then the only thing you could try to do is to say if a gene is 'expressed' or not, which is relatively uninteresting.

In other words, you might find that a gene is expressed in your patients, but so what? It may well be expressed at the same relative level in most other people as well, in which case it's just...normal?