Please help: perMANOVA using adonis2 on RNA-Seq data

[echo4922]

I am a beginner and I am trying to perform a perMANOVA test on RNA-Seq data.
Because it is not an ecology data, the snippet of RNA-Seq data looks like the following:

where the first column is gene id then three biological replicates for control (column 2 to column 4) then three biological replicates for treatment (column 5 to 7). Please note that the RNA-seq data has been log transformed.

Looking at Vegan manual, dune.env acts as meta data for data dune.

My question is how should I format my RNA-seq data such that I can create dune.env data as meta data to perform perMANOVA analysis?
Thank you.

[gavinsimpson]

Your data needs to be transposed relative to how you have it. You want genes in the columns and samples in the rows. That would be the equivalent of dune

You should also create another sheet with the sample ids in column 1 and the treatment info in column 2 and rep in column 3 for example. This would be the equivalent of dune.env.

In both cases you want the sample ID information to be stored as the rownames of the two respective data frames.

Other than that, consult any good introduction to base R to see how to read the data into R (that's not a vegan issue).