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Todos

final checklist

  • index / description
  • outline
  • day1
  • day2
  • day3
  • day4
  • summary / template

day 1

  • RColorBrewer example
  • recommendation windows -> workbench
  • no git -> download repo zip as alternative.

day 2

  • phrasing of question,
  • write_tsv instead of write_table
  • DESeq workflow -> a,b,d,e
  • before writing table, include resultsNames to get the coefficients printed out
  • possibly skip relevel() --> extensive contrast discussion

day 3

  • celltype + condition + celltype:condition --> fix manual explanation of beta (JJ<->BM)
  • use "real" sample names from data, rather than sample1,2,...
  • after break (heatmap of significant genes): - subset(padj < 0.05) is optional - simplify filter (%in%) - simplify heatmap (keep only scale = "row", everything else is optional)
  • skip results() in favour of lfcShrink()
  • mod_mat trick: - move up? - have a task/poll to create complex contrast: BM_DMSO vs JJ_TG
  • GENEID --> SYMBOL task too challenging.
    • needs more time or hints
    • columns selection: dplyr::select(8,9,10,14,15,16) --> select by pattern ?
  • reduce to only one prior gene set apoptosis or spliceosome

general todo

  • continuous variable in design ?
  • give example with own sizefactors (e.g. from spike-ins)?
  • enforce consistency in sample naming (DMSO or CTRL)