DESeq Without replicates 4 samples

[BFM]

Hi i am using DEseq with no replicates

i have four sample "A-Mock", "A-Infect", "B-Mock", "B-infect" with no replicates.

> conds <- factor( c( "A-Mock", "A-Infect", "B-Mock", "B-infect" ) )

i need to compare the diff expression between A-mock and A infect similarly B mock B infected. It doesnt seem to work i am using

res <- nbinomTest( cds, "A-mock", "A-infect", )
> res <- nbinomTest( cds, "B-mock", "B-infect", )

but at the end i am getting only one p value. How to solve this problem. Please help

[dpryan]

Since you don't have replicates, I wouldn't be surprised if that's the correct results. Any p-value from an unreplicated experiment like that will be questionable at best.

[BFM]

yes i know that, but what would be a good way to filter the differentially expressed genes between control and treatment then. Should i just go with fold change/? if yes please explain a bit about how i am quite new in NGS. Thank you

[dpryan]

Have a look at GFOLD, which you might find useful.