Thank you for your review and clarifying the statistical dimension of Amplicon analysis. Although I'm following through with most concepts, when it comes to the adaptation of the R code, I'm having some problems.
Simply running the R code with the sample data does not result in reproducible graphs. There are many errors that I've encountered throughout. I'm presuming that this is due to the updated arrangements of R and the affiliated packages.
I would love to implement the novel approaches mentioned in your review paper in my new research paper, however, I'm finding it quite challenging to implement since the code will not even work for your provided dataset, let alone my input that might be slightly different.
The ALDEx2 graphs seem to be working just fine and are reproducible when it comes to the Review Paper. However, problems arise when
Running f.t <- aldex.ttest(f.x, conds)
Doing PCA Plots.
Would very much appreciate if an updated R script could be implemented for the newest versions of R.
Dear Professor Gloor,
Thank you for your review and clarifying the statistical dimension of Amplicon analysis. Although I'm following through with most concepts, when it comes to the adaptation of the R code, I'm having some problems.
Simply running the R code with the sample data does not result in reproducible graphs. There are many errors that I've encountered throughout. I'm presuming that this is due to the updated arrangements of R and the affiliated packages.
I would love to implement the novel approaches mentioned in your review paper in my new research paper, however, I'm finding it quite challenging to implement since the code will not even work for your provided dataset, let alone my input that might be slightly different.
The ALDEx2 graphs seem to be working just fine and are reproducible when it comes to the Review Paper. However, problems arise when
Running f.t <- aldex.ttest(f.x, conds) Doing PCA Plots. Would very much appreciate if an updated R script could be implemented for the newest versions of R.
I've attached my RStudio console errors, objects, and graphs(https://drive.google.com/drive/folders/1Ugl3v9XP0p5AhdTgoSprcXIMbsOPDFzu?usp=sharing) My versions are:
R 4.1.1 RStudio 1.4.1717 ALDEx2 1.24.0 car 3.0-11 carData 3.0-4 CoDaSeq 0.99.6 zCompositions 1.3.4 igraph 1.2.6 grDevices 4.1.1 propr 4.2.6 vegan 2.5-7 Best, Erfan