Error in 'differential_abundance'
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strep • 0
@688ee615
Last seen 4 months ago
United Kingdom

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 :)

phyloseq devtools • 189 views
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y - ymean is not coming from anywhere in DESeq2 codebase, so I can't say the origin of the error.

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