I am facing a problem with differential expression analysis, were due to the intrinsic features of the samples we can't have replicates in one condition.
Study design: We have a patient with a very rare translocation , no other similar translocation has been described in the world and we expect that expression of the genes surrounding the translocation is altered. Hence, we have perform RNA-seq of the translocated patient and 4 controls.
How should I proceed?:
Before you kill me for asking "Can I do differential expression without replicates?", I known that EdgeR and DEseq2 provide ways to proceed without replicates , and that NOISeq could be used without replicates. However, in this case we have replicates for the controls were the biological variance of each gene could be estimated, but no for the the patient, as there is no other individual in the world. So, my question is: Is there any way of estimating the variance for the control group, and then compare to the expression in one single sample, the patient in this case? Or better, do a dispersion estimation for the translocation patient?
my options (From EdgeR docs):
- Use the genes and transcripts that are far away or in other chromosomes than the chromosome with the translocation to estimate the dispersion of that sample
- Use a dispersion value defined previously.
Have any of you faced a similar problem, and, furthermore, have anybody tested how do the two options above mentioned that EdgeR provide for working without replicates perform?
thanks for reading :)