GitLab

• separate protein groups
• report 0-proportions similar to NAs
• expose renaming scheme as an argument
• protein_acc extraction depends on study (with/witnout name, w/o separator). Need to generify protein_acc=str_split_fixed(protein_ids, "[|]", 3). One way: --extract extrac_acc.R which defines extractor function -> protein_acc=extract_fun(protein_ids)
• detect presence/absence of identifcation types --> conditionaed executino of corresponding bits
• try to postpone annotation handling to end of data-prep workflow/analysis
• fix result table links #' [identSummary](r add_prefix("ident_types_summary.txt"))
• How to auto-adjust imputation proportion?
• We just need imputation because we want an abundance matrix for limma. for t-tests neither na->0 nor impuations are required because we can work with long data.

limma

• also show batch-corrected qc plots (clustering, pca)
• man muss das mal alles durchschauen
• why does the voom with a ~condition design fix the sample clustering in file:///Volumes/project-stepien/stepien_ms_fractions/data/limma/p_vs_s/dge_limma.html
• add condition/sample colors to voom vs raw plot
• externalize annotation of results
• why do ma plots look so weired?