fluffy-adventure

Automated version of MTXQCvX2 - fluffy adventure

Version and updates

2019-04-25 - minor update

Version: 1.0.8

Updated:

• MTXQCvX_part4: Check if metabolite names have been updated in config_mtx/conversion_metabolite.csv
• Experimental_setup: Red subtitles to highlight content that should be updated ;)

2019-04-22 - major update

Version: 1.0.7

Updates:

• MTXQCvX2_part3: Automated detection of updated / manually validated MIDs
• MTXQCvX2_part3: Integration of metmax-based projects for manual data validation
• Minor bug fixes and code cleaning across MTXQCvX2

Please download the current version and rerun MTXQCvX_part3 in your MTXQC-projects if used.

2019-03-29 - major update

Version: 1.0.6

Updates:

• Update of Quant definitions: new Quant_v5
• Minor bug fixes in MTXQCvX2_part1
• Correction metabolite names in conversion_metabolite.csv

2019-02-10 - minor update

Checked MTXQCvX2 throughfully and added further datasets to play with MTXQCvX2 in combination with the MTXQCvX2 documentation.

2019-02-04 - major update

Version: 1.0.5.910

I corrected the reading of the ManualQuantTable information in MTXQCvX2 part 1 subsequently running Metmax integration (part 4).

Checked with maui and metmax input.

Please stay tuned for further refinements in the next couple of hours!

2018-12-03 - minor update

Verion: 1.0.5

Updates:

• Export of lowQ and highQ MIDs in MTXQCvX_part3 - ManualValidation for incorporation data

2018-10-30 - major update

Verion: 1.0.4

Updates:

• added a list of metabolite abbreviations at the end of MTXQCvX2 part1 and part2
• minor bug fixes in graphs

2018-10-24 - major update

Version: 1.0.3.901

another bug fixed. Esstial for additional quantification standards.

Version: 1.0.3.900

MTXQCvX_part3 I corrected the integration of manually validated MIDs and original MIDs (pSIRM_SpectraData.csv). Previoulsy the corrected MIDs have been integrated into the table containing only the lowQ MIDs, the file that has been generated as template to add corrected MID values. In consequence the lowQ/goodQ plot did not include the goodQ MIDs after re-processing MTXQCvX_part1.

The determination of the isotope incorporation hasn't been incorrect, though. This is done in a separate process and has been correct before.

Anyhow - please download the new version.

2018-10-22 - major update

Version: 1.0.3

I have included first files of documentation in the folder man/vignettes. You need to knit each .Rmd. file in order read these files in a comfortable format. You might to need to run install.packages("tufte") prior rendering a file.

Furthermore I have implemented smaller bug fixes, typos and such kind of things.

2018-10-16 - major update

Important fix in case you have issues with MTXQCvX2_part3 - ManualValidation of PeakAreas

Integration of warning messages if you have the following issue:

• multiple values for a single metabolite and file in ManVal_PeakAreas.csv
• resulting in a warning: aggregation function missing
• cause a malfunction of the integration of peakareas into original file

The fix shows now detailed warning messages and where to check to fix the issue.

If warning occurs:

• check Aggregationfailure.csv file created in project-folder/output
• mean_val reflects average value for metabolite across the project
• mean_val shows values in single, double digits: these are duplicated values
• fix these duplicates values per metaboltie and file in ManVal_PeakAreas.csv
• Re-do Integragtion of peakareas

2018-10-15 - major update

Quick fix

Correction of file name after integration of incorporation data performed by MTXQCvX2_part3.

Issue:

• wrong file name pSIRM_Spectra_man.csv
• correct: pSIRM_SpectraData_man.csv

Please download a new zip-file of MTXQCvX2!

2018-10-15 - minor update

I updated the error messages and actual catching errors related to ManualQuantTable.tsc-files.

In detail MTXQCvX2_part1 checks now if you have renamed ManualQuantTable.tsv and if not, it exits the processing of your data. A related FATAL ERROR is shown in the pdf and directs you what to do in order to solve this issue.

I hope it helps!

2018-10-08 - minor update

Update:

• Renaming of cinnamic acid related entries to internal standard
• accordingly updated MTXQCvX_part1 and part2, as well as R functions
• minor adjustments of plotting settings in MTXQCvX part2

2018-10-05 - major update

Update:

• Major corrections and modifications in MTXQCvX2 part 2
• Restructure of internal R functions organisation
• Integration of color styles

2018-09-27 - major update

comment: Please download a new copy of the MTXQCvX2

I updated the following:

• MTXQCpart4: tracing empty data frames for internal standard
• MTXQCpart1: tracing missing statistics: internal standard or sum of area
• conversion_metabolite.csv: replaced value 99 in Mass_Pos

2018-09-25 - publication of repository

Description

This current state includes fully automated Rmd-reports for Metabolomics projects.

Technical details

Input formats

Currenty supported input formats:

• Maui
• Metmax
• Spreadsheet (under dev)

Implemented modules

MTXQCinit

MTXQC Experimental setup

Parameter of the report:

• subfolder: text
• input: [metmax, maui]
• file annotation: e.g., annotation.csv
• sample extracts definition: e.g., Sample_extracts.csv
• kind of experiment: [qMTX, pSIRM, pSIRM timeseries]
• stable isotope: [none, glc, gln, pyr, other]
• InternalStandard: [none, cinnamicacid, other]
• origin: [blood, cell extracts, tissue, mixed]
• additional calibration: [no, yes]
• Quant-Mix: [Quant1_v3, Quant1_v4, Quant1_indv]
• Technical replicates: text

MTXQC part1 - QC

Parameter of the report:

• subfolder:
• input: [metmax, maui]
• Manual Validation: [none, all, PeakAreas, Incorporation]

MTXQC part2 - Post-Processing

Parameter of the report:

• subfolder:
• analysis: [stringent, less_stringent]
• InternalStandard: [True, False]
• Value of your choice:
• Parameter 1:
• Parameter 2:
• Parameter 3:
• Parameter 4:
• Manual Validation: [none, all, PeakAreas, Incorporation]

MTXQC part3 - Manual Validation

Parameter of the report:

• subfolder:
• output folder:
• transform: [none, PeakArea, Incorporation]
• integration: [none, PeakArea, Incorporation]
• input formatL: [metmax, maui]

MTXQC part4 - Metmax integration

Parameter of the report:

• subfolder: text
• PeakAreaMatrix: file-definition
• m73-data: file-defintion
• MIDs: file-definition
• InternalStandard: [True, False]
• Generate Alkane: [True, False]
• Generate SumOfArea-normalisation: [True, False]
• Generate ManualQuantTable and samples peakareamatrix: [True, False]
• Calculate incorporation: [True, False]