Hey,

Had something really strange happen to me when running my normal DESeq2 work flow. The counts function is giving the error message:

Error in UseMethod("counts") : no applicable method for 'counts' applied to an object of class "c('DESeqDataSet', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'Vector', 'Annotated', 'vectorORVector')"

This even occurs when I run the example from https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/counts

Input:
dds <- makeExampleDESeqDataSet(m=4)
head(counts(dds))

Output:
Error in UseMethod("counts") : 
no applicable method for 'counts' applied to an object of class "c('DESeqDataSet', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'Vector', 'Annotated', 'vector_OR_Vector')"

Does anyone know what may be happening here? I loaded appropriate libraries and restarted my R session.

Thanks!

Something may be wrong with your installation of Bioconductor packages. I'd recommend restarting, then re-installing your Bioconductor packages. You can also assess if you have a valid installation:

https://www.bioconductor.org/install/#troubleshoot-bioconductor-packages