DeSeq2 analysis of samples with no replicates?

Question

[Meeran]

Hi,

I am interested in performing Differential gene expression analysis of samples with no replicates (one control vs one treated). Is it possible to perform this using DESeq2 tools? If yes, Kindly suggest me the method to perform this analysis.

[iraun]

I guess that you have already read in the hundreds of previous posts similar to this one, that this is not a recommended practice, since your results will have no statistical relevance. Having said this, I think old versions of DESeq2 allow the analysis without replicates, or you could try other tools like NOISeq.

[Meeran]

Oh ok Thank you so much

Answer 1

[cpad0112]

Deseq2 doesn't allow such a setup. Try edgeR. In edgeR manual, there is a dedicated section for experiments with no replicates.

[Kevin Blighe]

The section in question is: 2.12 What to do if you have no replicates

edgeR is primarily intended for use with data including biological replication. Nevertheless, RNA-Seq and ChIP-Seq are still expensive technologies, so it sometimes happens that only one library can be created for each treatment condition. In these cases there are no replicate libraries from which to estimate biological variability. In this situation, the data analyst is faced with the following choices, none of which are ideal. We do not recommend any of these choices as a satisfactory alternative for biological replication.

...and then lists the choices available.

Reference: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf