Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
Hello,
I have two questions:
Is Z-scaled data or Pareto-scaled counts data from RNA-Seq appropriate as input into WGCNA (or the multiWGCNA package (if this is known))?
I have tried using multiWGCNA to analyze RNA-Seq data across two strains and two tissue types. I have rownames that correspond to ENSEMBL IDs but I'm getting the error:
error in .rownamesdf<-(x, value = value) : duplicate 'row.names' are not allowed.
I have checked that each row has a unique ID by using the function
rownames(df) = make.names(rownames(df), unique = TRUE)
and have separately added unique numbers to each ID to 'tag' it.
Please advise on why this might be happening if possible!
Best, shasabhi1
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What function do you run to get the error?
I get the same error when running the constructNetworks function - I've also made sure that all gene IDs and sample names are unique
I can run the example datasets without error