Skip to content
Permalink
main
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

superShiny/README.md

Go to file
 
 
Cannot retrieve contributors at this time
superShiny 2024 Input Parsing Work steps Newest Bug yeti
46 lines (31 sloc) 1.17 KB
Raw Blame
Open in GitHub Desktop

superShiny 2024

Input

Excel file with the following sheets

  • SAMPLE
  • MEASUREMENT
  • FEATURE (optional, because of old format)

FEATURE currently not supported

Parsing

  1. Feature names are split. Internal standards are identified and base compounds name extracted
  2. Measurement data frame is prepared for normalisation. Internal standards, biological normalisation, TIC and associated standard all possible

Work steps

  1. Input from server or old school. Server part rewritten.
  2. Standard: display all available normalisation variables
  3. PCA: normalise and display PCA
  • pca figure size to global preferences
  • my_proc$res created already by parse
  • check 'baseline'
  • check correlation check
  • create input file with pools
  • create input file mz/rt
  • compound db with plot order

Newest

  • Keep pool samples
  • Pool samples may have missing values in experimental design columns
  • Pool samples may have missing values in normalisation columns (replaced by mean)

Bug

  • when last outlist item is removed, my_proc$outlist == NULL, does not update

yeti

  • Overhauled Infile tab error messages
  • Load custom comp_db
  • Overhauled Stan tab plot appearance options