I'm interested in comparing the levels of certain transcripts from an experimental time point versus a control time point. However, whenever I run DESeq2 on the counts table, it throws this error:

estimating size factors estimating dispersions Error in checkForExperimentalReplicates(object, modelMatrix) :

The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was deprecated in v1.20 and no longer supported since v1.22.

Calls: DESeq ... estimateDispersions -> .local -> checkForExperimentalReplicates Execution halted

Is there an easy work around for this? I'm simply looking to see if there's a relative change from time point to time point.

Thanks for any help you can give.

You can use a design of ~1