Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames

Question

[shasabhi1]

Hello,

I have two questions:

1. 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))?

2. 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

[allingt]

What function do you run to get the error?

[James]

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