Slight documentation improvements (for me a first time user)

[bednarsky]

Here, I collect some things that I found confusing. I think it never hurts to deconfuse the user as much as possible (even though many things could be clear I guess, but why not make it easy)

• group in filter_parameters. → Add comment: group is a column in annotation
• reCombat_parameters norm_methods: Which methods can I use from above how? Default ["CQN", "TMM"] suggests that I use uppercase letters, but I have to guess. e.g., would this work? ["TMM", "VOOM", "RLE", "none"]? → provide all options in comment as list if possible? Or explain how they come about? → this one was also hard to resolve with looking into the code, e.g., for "none" in edgeR_parameters: method: I think I should use "CPM" in my case (edgeR_parameters: quantification:) instead of "none"
• Since you collect best practices here that also include knowledge, some words on whether it makes sense to use VOOM and then reCombat (or similar combinations) would be nice → it's not in the defaults and I don't understand why.

  • if you are using limma-trend you start with normalized data, that's why I was not thinking of voom. voom I just added so the user gets a feeling how the data actually looks inside of a limma-voom approach.

[sreichl]

Good issue/effort. let's collect until you are done with the first time usage and then I can incorporate it into the docs.