Ions - Samples Re-Run

[amyerspigg]

Several ions did not pass visual/logical value tests after the EC1 workshop. After manual investigation of the values, we are re-running samples in this file: Data/ions/EC1_ions_rerun.csv

To Do for @opalotenburg @kaizadp @amyerspigg :

• Rerun samples at lower dilution
• Merge new data with older data at higher dilution (e.g. for Cl-)
• Update ions readme
• Update ions file
• Ions charge balance calculations (not doing)

[kaizadp]

AMP, OO, KFP discussion

dealing with dilutions craziness

• match the results with the dilutions and dates
• for the required dilutions in the dilution-key, there may be multiple dates
• choose the most recent date

@opalotenburg just needs to send @kaizadp the new dilution file

[stephpenn1]

• Re-run ions code
• Make L0B
• Make L2
• Upload to GDrive

[amyerspigg]

Issues with NAs introduced with dilution level chosen

EC1_K036 | 2022-11-03 | sodium | 5.881014 | NA | NA | 300
EC1_K036 | 2022-10-03 | sodium | 76.472898 | NA | NA | 25
EC1_K036 | 2022-02-11 | sodium | 36.527696 | NA | blank correct | 50

[amyerspigg]

Somewhere between raw_data, data_ions_processed and data_ions_qc LOST a whole run date (20221019)

Date is in the ions_lods dataframe though

Check out this error in line 446
Warning message:
In left_join(., QC_DATA %>% dplyr::select(Ion, date_run, LOD_ppm)) :
Each row in x is expected to match at most 1 row in y.
ℹ Row 4819 of x matches multiple rows.
ℹ If multiple matches are expected, set multiple = "all" to silence this warning.

[stephpenn1]

date run 2022-02-18 have duplicate entries. we only read the files in once , so duplicates were introduced somewhere between raw data and data_ions_qc

[stephpenn1]

date run 2022-02-18 have duplicate entries. we only read the files in once , so duplicates were introduced somewhere between raw data and data_ions_qc

update: duplicates are introduced because there is duplicate files. SP asked @opalotenburg which one should be used and code will be re-run when its decided

[amyerspigg]

some ions are over or under diluted without the correct dilution level available. need to compile list of these to re run in instrument at correct dilution level for that ion.

[kaizadp]

2024-02-07
AMP, SCP, KFP

1:
looked at flags for samples. not rerunning samples for ammonium, lithium, fluoride, phosphate (these are low concentrations and likely to be below detect even at 1x detection.

K037 is missing nitrate values at 1x. this sample was run at 1x, but was flagged "omit" in the readme file. need to double-check if this meant omit for all or for just the other detectors?

2:
decision for L2: when we move to L2, put each analyte in a different csv, and zip all files under "ions"

@amyerspigg

[amyerspigg]

K037: Use UV detector from the 1x dilution
Use 50x dilution for other ions