Hi everyone

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

It would help to know what the levels of the factors in your design are, so to give advice how you can change them. Does the message make sense? The levels need to be unique, so try only using letters and number, not symbols, which are removed by R's make.names() function.