I am having a bit of trouble interpreting a result after running DESeq2 on an RNA-seq dataset with 6 biological replicates for multiple conditions (comparing a parental cell line and multiple independent gene KOs). In particular, for a couple genes I am observing Pvalues of 0, which I interpret as them being even smaller than the closest numeric Pvalue listed of "2.18E-269" (I know, incredibly small). I have independent validation that these genes with Pvalues of 0 are real changes, so it seems logical that I'd be able to plot them in a traditional volcano plot after -log10 transformations, but this transformation obviously doesn't work when the Pvalue=0.
I have seen similar topics discussed in other forums, but haven't seen an exact solution to this problem. Should I re-run the analysis with different parameters so that I have more believable Pvalues? Or should I be imputing values in place of the 0?