- index / description
- outline
- day1
- day2
- day3
- day4
- summary / template
- RColorBrewer example
- recommendation windows -> workbench
- no git -> download repo zip as alternative.
- 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
- 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
- continuous variable in design ?
- give example with own sizefactors (e.g. from spike-ins)?
- enforce consistency in sample naming (DMSO or CTRL)