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# System prepended metadata

title: Backlog / issues

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# Backlog / issues

## Pipeline
* `bbAlign`: Determine where "No_fill" peak table should be taken from. 
    * Before hard fill or after hard fill/before imputation?
    * How to evaluate? Somehow by checking NA-values...
    * _Date added_: 2024-06-04 (AR)

* `driftCorr`: Scaling of variables, which order to do things:
    * After within-batch drift correction
    * Anton/Calle pseudocode to manage zeros and missingness (see issue with "Problems with 0z in dataset")
    * _Date added_: 2024-06-04 (AR)

* Problems with 0z in COSMC dataset
    * Arises from imputation - mvImpWrap bug fixed 2024-06-04 (CB)
    * What to do?
        * Set `pp_imp[pp_imp < 0 ] <- 0`
        * perform `bbAlign` 
        * Per batch
            * `batchCorr`
            * imputeSubZero from batchCorr with `mvImpWrap`
            * Feats which are 100% 0s are flagged
            * rnorm() to give a spread for normalization not to break
            * scale from zero (CB: I don't understand what this means)
        * merge batches
        * normalize batches
        * remove flagged values (entire features within batches)
        * impute missing values (i.e. systematic imputation of en entire feature within specific batch(es))
    * _Date added_: 2024-06-04 (AR)

* IPO2 rtAlign optimization
    * None-existent, there is no way to process using xcms4 while this problem persists
    * _Date added_: 2024-06-06 (AR)

* IPO2 PP optimization
    * Should be xcms4 according to Calle
    * _Date added_: 2024-06-06 (AR)

* Parallelization of plotClust
    * One pdf takes 6 hours to generate in COSMC
    * Faster plotting + parallelization is needed
    * _Date added_: 2024-06-06 (AR)

# Fixed issues

* `mvImpWrap()`: Gives negative values, even with `forceZero = TRUE`
  * Isolate bug: Second round mvImp in mvImpWrap was missing the forceZero argument
  * Fix: Added forceZero argument to 2nd round mvImp in mvImpWrap.
  * Additionally: Added some more output and cleaned up some code
  * _Date added_: 2024-06-04 (CB)
  * _Date fixed_: 2024-06-04 (CB)