Hi there - asking for some help with an error that has come up using the 'differential_abundance' command. (nb: I am a beginner)
I have my code
differential_abundance(physeqDE, grouping_column = "Compartment", pvalue.threshold = 0.05, lfc.threshold = 0, filename = F, output_norm = "log-relative")
And I get the output error
converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 4 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing Error in y - ymean : non-numeric argument to binary operator In addition: Warning messages: 1: In DESeqDataSet(se, design = design, ignoreRank) : some variables in design formula are characters, converting to factors 2: In randomForest.default(m, y, ...) : The response has five or fewer unique values. Are you sure you want to do regression? 3: In mean.default(y) : argument is not numeric or logical: returning NA
I have a colleague who has used this command in the past and it has worked for them but they get the same error as well when they run their code, whilst still on their original environment too.
Any help would be appreciated :)