MassSpec Workflow Improvemnts
- separate protein groups
- report 0-proportions similar to NAs
- expose renaming scheme as an argument
protein_accextraction 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.Rwhich defines extractor function ->
- 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](
- 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.
- also show batch-corrected qc plots (clustering, pca)
- man muss das mal alles durchschauen
- why does the voom with a
~conditiondesign fix the sample clustering in
- add condition/sample colors to voom vs raw plot
- externalize annotation of results
- why do ma plots look so weired?