DESeq2 counts function not working
1
0
Entering edit mode
mrfossl97 ▴ 10
@mrfossl97-20728
Last seen 4.3 years ago

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!

deseq2 Deseq RNAseq • 1.2k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 4 hours ago
United States

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

ADD COMMENT

Login before adding your answer.

Traffic: 812 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6