Hello,

I'm working on a RNAseq dataset with two passages and no replicate!

the STAR-HTSeq output with any of:

dds <- DESeq(ddsHTSeq)
dds <- DESeq(ddsHTSeq, minReplicatesForReplace=Inf, betaPrior=T, modelMatrixType="expanded")
dds <- DESeq(ddsHTSeq, betaPrior=T, modelMatrixType="expanded")
dds <- DESeq(ddsHTSeq, minReplicatesForReplace=Inf)

then something like resDF_DW_P2 <- results(dds, contrast=c("group", "DF1_P2", "DW2_P2"), ref= "EV_P2") gives the DEG list with padj values ~0.99.  

was wondering which one is the correct option to proceed. 

would you think it is correct if I only consider the p-values instead of p-adj values?

Many thanks

Mahtetie

It's not surprising that there is no significance with no replicates, this is discussed in this paragraph in ?DESeq:

"Experiments without replicates do not allow for estimation of the dispersion of counts around the expected value for each group, which is critical for differential expression analysis. ... We provide this approach for data exploration only, but for accurately identifying differential expression, biological replicates are required."

You should not use unadjusted p-values.

DESeq(2) and edgeR are not intended to be used with designs with less than 3 replicates. For those designs, NOIseq or GFOLD may be better choices, but it's still not a good idea to draw conclusions based on their results.