I am trying to use DESeq2 on a Phyloseq object and am running into a consistent error.
I've followed all the online tutorials, however whenever I get to the stage to run "phyloseq_to_deseq2" I get the following error:
invalid class “DESeqDataSet” object: levels of factors in the design have non-unique level names after make.names() is applied. best to only use letters and numbers for levels of factors in the design
If anyone has any experience with this error or knows what I am doing wrong I'd really appreciate any help
thanks in advance