DESeq2 error

Question

[sooni]

I am currently trying to create pseudo-bulk data from single cell RNA data and perform DE analysis using DESeq2.

dds_Bcell <- DESeq(dds_Bcell)

When I run the above code, the following error occurs:

The following error occurred 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.

I think the reason this error occurs is because there is only 1 sample per group in my single cell RNA data. There are a total of 3 groups in my single cell RNA data. How can I run the DESeq() function when there is 1 sample for each group? Or is DESeq2 analysis not possible in this case?

Thank you for help!

Answer 1

[ATpoint]

At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.