In some specific situations, it is neither affordable nor feasible to have replicates for large RNA-seq analysis. Moreover, the analysis purpose is just hypothesis generation for further experiment design. So, is it possible to have duplicate samples for one or two of the groups and use one sample for other groups? Could we estimate a constant dispersion from these replicates and apply it to all of the samples for differential gene expression analysis.
EdgeR/Limma for my differential gene expression analysis. When there are no replicates the
eBays function gives me an error. However, if I add replicate to just one of the samples, it won't give any errors. Does this mean that it uses the calculated dispersion from the duplicate condition for all of the other one sample conditions? Or is it a bug that it doesn't give an
Should I consider this method of using duplicates for some samples instead of just using no replicates in such large experiments that are being done for hypothesis generation?