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  • #28

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Created Dec 07, 2018 by brandl@brandlOwner7 of 9 tasks completed7/9 tasks

ms_workflow: Improvemnts

  • 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? image
Edited Dec 10, 2019 by domingue
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