Hello,

While running the eisaR program with three biological replicates each for control and treated samples instead of two replicates (as shown in the vignette), is there any change to be made in the program? Can it be done in the default mode, i.e., "Run eisa convenienty?" This approach resulted in error due to which I switched to "run eisa step-by-step" mode. In this approach, I got the following error:

> y <- estimateDisp(y, design)
Warning message:
In estimateDisp.default(y = y$counts, design = design, group = group,  :
  No residual df: setting dispersion to NA
> fit <- glmFit(y, design)
Error in glmFit.default(y = y$counts, design = design, dispersion = dispersion,  : 
  NA dispersions not allowed

Kindly guide me as to how to rectify this issue and what changes need to be made in the command.

Thank you

Regards Nishanth

You have most likely setup up the design matrix incorrectly.

You don't shown us how you created the design matrix, so we can't tell what you might have done wrong. When you post a question here you need to give all the code necessary to create the error, not just one or two commands in isolation with undefined input arguments. See https://www.bioconductor.org/help/support/posting-guide/