This isn't entirely a bioinformatic related question but if anyone has any input it would be greatly appreciated.
I have 3 libraries, each of the same FACS sorted cells, under the same conditions, with the difference that each library was done on cells isolated at different time points, and we don't have replicates. I've generated count files for each of the libraries but I'm having issues as to how to lay them out into deseq2 on galaxy.
My initial approach was to set them all out under the same Factor name, in different factor levels:
E.g Factor name: Neurons Factor level 1: 3h 2: 6h 3: 12h
But that layout seemed to not be working out that well all the outputs seemed odd as it was skipping factor level 3 in the comparison.
I tried setting each time point under a different factor name but the issue there is that Deseq2 required at least 2 factor levels for each factor name.
Any suggestions how to go about analysing this?