I'm using Cufflinks-Cuffdiff to get the differentially expressed genes in two samples, the thing is for some genes where their expression level in one of the two samples is 0 I get extreme (weird) values of the log2(fold change) (I guess as a result of either dividing by 0 or calculating the log2 of 0). What do you usually do with these genes? do you discard them or do you keep them for downstream analysis?
Here you are an example of what I mean (the columns would be gene name, FPKM in sample 1, FPKM in sample 2, log2(fold change)
OR4F16 0 0.00245667 1.79769e+308
EDITED: Would you trust on the p-value obtained in these cases?