I am trying to run DESeq2 using HTseq count as input but I am running in the following error every time, I already checked and input data is correct.
2 samples with counts over 18838 genes
using disperion fit type: parametric
estimating size factors
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 → DESeqParallel → checkForExperimentalReplicates
I have SINGLE file per treatment (two treatments) and they have same number of lines (outpu htseq)